Starting phenix.real_space_refine on Tue Aug 26 19:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9op5_70679/08_2025/9op5_70679.cif Found real_map, /net/cci-nas-00/data/ceres_data/9op5_70679/08_2025/9op5_70679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9op5_70679/08_2025/9op5_70679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9op5_70679/08_2025/9op5_70679.map" model { file = "/net/cci-nas-00/data/ceres_data/9op5_70679/08_2025/9op5_70679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9op5_70679/08_2025/9op5_70679.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 25776 2.51 5 N 7296 2.21 5 O 7296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40476 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "a" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "b" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "c" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "d" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "e" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "f" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "g" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "h" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "i" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "j" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "k" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "l" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Time building chain proxies: 10.03, per 1000 atoms: 0.25 Number of scatterers: 40476 At special positions: 0 Unit cell: (160.6, 159.5, 156.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 7296 8.00 N 7296 7.00 C 25776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9432 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 46 sheets defined 61.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'a' and resid 33 through 45 removed outlier: 4.290A pdb=" N PHE a 39 " --> pdb=" O GLY a 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG a 40 " --> pdb=" O THR a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 54 Processing helix chain 'a' and resid 55 through 60 removed outlier: 3.589A pdb=" N VAL a 59 " --> pdb=" O VAL a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 80 removed outlier: 3.855A pdb=" N ALA a 80 " --> pdb=" O ALA a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 98 removed outlier: 3.533A pdb=" N LEU a 86 " --> pdb=" O THR a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 109 Processing helix chain 'a' and resid 112 through 144 removed outlier: 3.649A pdb=" N TRP a 127 " --> pdb=" O VAL a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 150 Proline residue: a 148 - end of helix No H-bonds generated for 'chain 'a' and resid 145 through 150' Processing helix chain 'a' and resid 156 through 167 Processing helix chain 'a' and resid 179 through 190 Processing helix chain 'a' and resid 192 through 198 removed outlier: 4.313A pdb=" N ARG a 196 " --> pdb=" O HIS a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 198 through 221 Proline residue: a 210 - end of helix Processing helix chain 'a' and resid 271 through 297 Proline residue: a 278 - end of helix removed outlier: 3.853A pdb=" N ASN a 297 " --> pdb=" O CYS a 293 " (cutoff:3.500A) Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.577A pdb=" N PHE a 540 " --> pdb=" O LEU a 536 " (cutoff:3.500A) Processing helix chain 'a' and resid 558 through 573 removed outlier: 3.703A pdb=" N ILE a 562 " --> pdb=" O SER a 558 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA a 563 " --> pdb=" O SER a 559 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA a 567 " --> pdb=" O ALA a 563 " (cutoff:3.500A) Proline residue: a 568 - end of helix Processing helix chain 'a' and resid 591 through 603 removed outlier: 3.790A pdb=" N LYS a 602 " --> pdb=" O ALA a 598 " (cutoff:3.500A) Processing helix chain 'a' and resid 603 through 623 removed outlier: 4.264A pdb=" N THR a 607 " --> pdb=" O THR a 603 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLN a 621 " --> pdb=" O VAL a 617 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS a 622 " --> pdb=" O ALA a 618 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA a 623 " --> pdb=" O ASP a 619 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 44 removed outlier: 4.281A pdb=" N PHE b 39 " --> pdb=" O GLY b 35 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG b 40 " --> pdb=" O THR b 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 54 Processing helix chain 'b' and resid 55 through 60 removed outlier: 3.571A pdb=" N VAL b 59 " --> pdb=" O VAL b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 80 removed outlier: 3.852A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 98 Processing helix chain 'b' and resid 100 through 109 Processing helix chain 'b' and resid 112 through 144 removed outlier: 3.625A pdb=" N TRP b 127 " --> pdb=" O VAL b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 150 Proline residue: b 148 - end of helix No H-bonds generated for 'chain 'b' and resid 145 through 150' Processing helix chain 'b' and resid 156 through 167 Processing helix chain 'b' and resid 179 through 190 Processing helix chain 'b' and resid 192 through 198 removed outlier: 4.244A pdb=" N ARG b 196 " --> pdb=" O HIS b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 198 through 222 Proline residue: b 210 - end of helix removed outlier: 3.781A pdb=" N THR b 222 " --> pdb=" O ALA b 218 " (cutoff:3.500A) Processing helix chain 'b' and resid 271 through 297 Proline residue: b 278 - end of helix removed outlier: 3.782A pdb=" N ASN b 297 " --> pdb=" O CYS b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 521 through 540 removed outlier: 3.511A pdb=" N PHE b 540 " --> pdb=" O LEU b 536 " (cutoff:3.500A) Processing helix chain 'b' and resid 558 through 572 removed outlier: 3.591A pdb=" N ILE b 562 " --> pdb=" O SER b 558 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA b 563 " --> pdb=" O SER b 559 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA b 567 " --> pdb=" O ALA b 563 " (cutoff:3.500A) Proline residue: b 568 - end of helix Processing helix chain 'b' and resid 591 through 602 removed outlier: 3.918A pdb=" N LYS b 602 " --> pdb=" O ALA b 598 " (cutoff:3.500A) Processing helix chain 'b' and resid 603 through 623 removed outlier: 4.411A pdb=" N THR b 607 " --> pdb=" O THR b 603 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR b 608 " --> pdb=" O ARG b 604 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN b 621 " --> pdb=" O VAL b 617 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS b 622 " --> pdb=" O ALA b 618 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA b 623 " --> pdb=" O ASP b 619 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 44 removed outlier: 3.766A pdb=" N MET c 37 " --> pdb=" O THR c 33 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE c 39 " --> pdb=" O GLY c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 54 Processing helix chain 'c' and resid 55 through 60 removed outlier: 3.673A pdb=" N VAL c 59 " --> pdb=" O VAL c 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG c 60 " --> pdb=" O TYR c 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 55 through 60' Processing helix chain 'c' and resid 62 through 80 removed outlier: 3.792A pdb=" N ALA c 80 " --> pdb=" O ALA c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 98 Processing helix chain 'c' and resid 100 through 109 Processing helix chain 'c' and resid 112 through 144 removed outlier: 3.758A pdb=" N TRP c 127 " --> pdb=" O VAL c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 150 Proline residue: c 148 - end of helix No H-bonds generated for 'chain 'c' and resid 145 through 150' Processing helix chain 'c' and resid 156 through 167 Processing helix chain 'c' and resid 179 through 190 Processing helix chain 'c' and resid 192 through 198 removed outlier: 4.365A pdb=" N ARG c 196 " --> pdb=" O HIS c 192 " (cutoff:3.500A) Processing helix chain 'c' and resid 198 through 222 Proline residue: c 210 - end of helix removed outlier: 3.830A pdb=" N THR c 222 " --> pdb=" O ALA c 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 271 through 297 Proline residue: c 278 - end of helix removed outlier: 3.774A pdb=" N ASN c 297 " --> pdb=" O CYS c 293 " (cutoff:3.500A) Processing helix chain 'c' and resid 521 through 541 removed outlier: 3.549A pdb=" N PHE c 540 " --> pdb=" O LEU c 536 " (cutoff:3.500A) Processing helix chain 'c' and resid 558 through 573 removed outlier: 3.567A pdb=" N ILE c 562 " --> pdb=" O SER c 558 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA c 563 " --> pdb=" O SER c 559 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA c 567 " --> pdb=" O ALA c 563 " (cutoff:3.500A) Proline residue: c 568 - end of helix Processing helix chain 'c' and resid 591 through 602 removed outlier: 3.970A pdb=" N LYS c 602 " --> pdb=" O ALA c 598 " (cutoff:3.500A) Processing helix chain 'c' and resid 603 through 623 removed outlier: 4.365A pdb=" N THR c 607 " --> pdb=" O THR c 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR c 608 " --> pdb=" O ARG c 604 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN c 621 " --> pdb=" O VAL c 617 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS c 622 " --> pdb=" O ALA c 618 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA c 623 " --> pdb=" O ASP c 619 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 44 removed outlier: 4.232A pdb=" N PHE d 39 " --> pdb=" O GLY d 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG d 40 " --> pdb=" O THR d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 54 Processing helix chain 'd' and resid 55 through 60 removed outlier: 3.536A pdb=" N VAL d 59 " --> pdb=" O VAL d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 80 removed outlier: 3.808A pdb=" N ALA d 80 " --> pdb=" O ALA d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 98 removed outlier: 3.682A pdb=" N LEU d 86 " --> pdb=" O THR d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 109 Processing helix chain 'd' and resid 112 through 147 removed outlier: 3.673A pdb=" N TRP d 127 " --> pdb=" O VAL d 123 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS d 145 " --> pdb=" O GLY d 141 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE d 146 " --> pdb=" O LEU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 150 No H-bonds generated for 'chain 'd' and resid 148 through 150' Processing helix chain 'd' and resid 156 through 167 removed outlier: 3.510A pdb=" N TYR d 160 " --> pdb=" O SER d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 190 Processing helix chain 'd' and resid 192 through 198 removed outlier: 4.307A pdb=" N ARG d 196 " --> pdb=" O HIS d 192 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 221 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 271 through 297 Proline residue: d 278 - end of helix removed outlier: 3.762A pdb=" N ASN d 297 " --> pdb=" O CYS d 293 " (cutoff:3.500A) Processing helix chain 'd' and resid 521 through 540 removed outlier: 3.515A pdb=" N PHE d 540 " --> pdb=" O LEU d 536 " (cutoff:3.500A) Processing helix chain 'd' and resid 558 through 573 removed outlier: 3.619A pdb=" N ILE d 562 " --> pdb=" O SER d 558 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA d 563 " --> pdb=" O SER d 559 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA d 567 " --> pdb=" O ALA d 563 " (cutoff:3.500A) Proline residue: d 568 - end of helix Processing helix chain 'd' and resid 591 through 602 removed outlier: 3.879A pdb=" N LYS d 602 " --> pdb=" O ALA d 598 " (cutoff:3.500A) Processing helix chain 'd' and resid 604 through 623 removed outlier: 3.724A pdb=" N TYR d 608 " --> pdb=" O ARG d 604 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN d 621 " --> pdb=" O VAL d 617 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS d 622 " --> pdb=" O ALA d 618 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 44 removed outlier: 3.613A pdb=" N MET e 37 " --> pdb=" O THR e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 54 Processing helix chain 'e' and resid 55 through 60 removed outlier: 3.645A pdb=" N VAL e 59 " --> pdb=" O VAL e 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 55 through 60' Processing helix chain 'e' and resid 62 through 80 removed outlier: 3.794A pdb=" N ALA e 80 " --> pdb=" O ALA e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 98 removed outlier: 3.593A pdb=" N LEU e 86 " --> pdb=" O THR e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 109 Processing helix chain 'e' and resid 112 through 147 removed outlier: 3.671A pdb=" N TRP e 127 " --> pdb=" O VAL e 123 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS e 145 " --> pdb=" O GLY e 141 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE e 146 " --> pdb=" O LEU e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 150 No H-bonds generated for 'chain 'e' and resid 148 through 150' Processing helix chain 'e' and resid 156 through 167 Processing helix chain 'e' and resid 179 through 190 Processing helix chain 'e' and resid 192 through 198 removed outlier: 4.169A pdb=" N ARG e 196 " --> pdb=" O HIS e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 198 through 221 Proline residue: e 210 - end of helix Processing helix chain 'e' and resid 271 through 297 Proline residue: e 278 - end of helix removed outlier: 3.816A pdb=" N ASN e 297 " --> pdb=" O CYS e 293 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 541 removed outlier: 3.513A pdb=" N PHE e 540 " --> pdb=" O LEU e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 558 through 573 removed outlier: 3.614A pdb=" N ILE e 562 " --> pdb=" O SER e 558 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA e 563 " --> pdb=" O SER e 559 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA e 567 " --> pdb=" O ALA e 563 " (cutoff:3.500A) Proline residue: e 568 - end of helix Processing helix chain 'e' and resid 591 through 603 removed outlier: 3.848A pdb=" N LYS e 602 " --> pdb=" O ALA e 598 " (cutoff:3.500A) Processing helix chain 'e' and resid 603 through 623 removed outlier: 4.412A pdb=" N THR e 607 " --> pdb=" O THR e 603 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR e 608 " --> pdb=" O ARG e 604 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA e 614 " --> pdb=" O THR e 610 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN e 621 " --> pdb=" O VAL e 617 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS e 622 " --> pdb=" O ALA e 618 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA e 623 " --> pdb=" O ASP e 619 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 44 removed outlier: 4.293A pdb=" N PHE f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG f 40 " --> pdb=" O THR f 36 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 54 Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.655A pdb=" N VAL f 59 " --> pdb=" O VAL f 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG f 60 " --> pdb=" O TYR f 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 55 through 60' Processing helix chain 'f' and resid 62 through 79 Processing helix chain 'f' and resid 82 through 98 Processing helix chain 'f' and resid 100 through 109 Processing helix chain 'f' and resid 112 through 144 removed outlier: 3.683A pdb=" N TRP f 127 " --> pdb=" O VAL f 123 " (cutoff:3.500A) Processing helix chain 'f' and resid 145 through 150 Proline residue: f 148 - end of helix No H-bonds generated for 'chain 'f' and resid 145 through 150' Processing helix chain 'f' and resid 156 through 167 Processing helix chain 'f' and resid 179 through 190 Processing helix chain 'f' and resid 192 through 198 removed outlier: 4.393A pdb=" N ARG f 196 " --> pdb=" O HIS f 192 " (cutoff:3.500A) Processing helix chain 'f' and resid 198 through 221 Proline residue: f 210 - end of helix Processing helix chain 'f' and resid 271 through 297 Proline residue: f 278 - end of helix removed outlier: 3.777A pdb=" N ASN f 297 " --> pdb=" O CYS f 293 " (cutoff:3.500A) Processing helix chain 'f' and resid 521 through 541 removed outlier: 3.550A pdb=" N PHE f 540 " --> pdb=" O LEU f 536 " (cutoff:3.500A) Processing helix chain 'f' and resid 558 through 572 removed outlier: 3.623A pdb=" N ILE f 562 " --> pdb=" O SER f 558 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA f 563 " --> pdb=" O SER f 559 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA f 567 " --> pdb=" O ALA f 563 " (cutoff:3.500A) Proline residue: f 568 - end of helix Processing helix chain 'f' and resid 591 through 603 removed outlier: 3.869A pdb=" N LYS f 602 " --> pdb=" O ALA f 598 " (cutoff:3.500A) Processing helix chain 'f' and resid 603 through 623 removed outlier: 4.245A pdb=" N THR f 607 " --> pdb=" O THR f 603 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR f 608 " --> pdb=" O ARG f 604 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN f 621 " --> pdb=" O VAL f 617 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS f 622 " --> pdb=" O ALA f 618 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA f 623 " --> pdb=" O ASP f 619 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 44 removed outlier: 4.430A pdb=" N PHE g 39 " --> pdb=" O GLY g 35 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG g 40 " --> pdb=" O THR g 36 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU g 41 " --> pdb=" O MET g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 54 Processing helix chain 'g' and resid 55 through 60 removed outlier: 3.653A pdb=" N VAL g 59 " --> pdb=" O VAL g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 80 removed outlier: 3.827A pdb=" N ALA g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 98 removed outlier: 3.582A pdb=" N LEU g 86 " --> pdb=" O THR g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 109 Processing helix chain 'g' and resid 112 through 144 removed outlier: 3.624A pdb=" N TRP g 127 " --> pdb=" O VAL g 123 " (cutoff:3.500A) Processing helix chain 'g' and resid 145 through 150 Proline residue: g 148 - end of helix No H-bonds generated for 'chain 'g' and resid 145 through 150' Processing helix chain 'g' and resid 156 through 167 Processing helix chain 'g' and resid 179 through 190 Processing helix chain 'g' and resid 192 through 198 removed outlier: 4.251A pdb=" N ARG g 196 " --> pdb=" O HIS g 192 " (cutoff:3.500A) Processing helix chain 'g' and resid 198 through 222 Proline residue: g 210 - end of helix removed outlier: 3.760A pdb=" N THR g 222 " --> pdb=" O ALA g 218 " (cutoff:3.500A) Processing helix chain 'g' and resid 271 through 297 Proline residue: g 278 - end of helix removed outlier: 3.833A pdb=" N ASN g 297 " --> pdb=" O CYS g 293 " (cutoff:3.500A) Processing helix chain 'g' and resid 521 through 541 Processing helix chain 'g' and resid 558 through 573 removed outlier: 3.669A pdb=" N ILE g 562 " --> pdb=" O SER g 558 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA g 563 " --> pdb=" O SER g 559 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA g 567 " --> pdb=" O ALA g 563 " (cutoff:3.500A) Proline residue: g 568 - end of helix Processing helix chain 'g' and resid 591 through 603 removed outlier: 3.833A pdb=" N LYS g 602 " --> pdb=" O ALA g 598 " (cutoff:3.500A) Processing helix chain 'g' and resid 603 through 623 removed outlier: 4.419A pdb=" N THR g 607 " --> pdb=" O THR g 603 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR g 608 " --> pdb=" O ARG g 604 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN g 621 " --> pdb=" O VAL g 617 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS g 622 " --> pdb=" O ALA g 618 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA g 623 " --> pdb=" O ASP g 619 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 44 removed outlier: 3.778A pdb=" N MET h 37 " --> pdb=" O THR h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 54 Processing helix chain 'h' and resid 55 through 60 removed outlier: 3.609A pdb=" N VAL h 59 " --> pdb=" O VAL h 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG h 60 " --> pdb=" O TYR h 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 55 through 60' Processing helix chain 'h' and resid 62 through 80 removed outlier: 3.824A pdb=" N ALA h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 98 removed outlier: 3.505A pdb=" N LEU h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 109 Processing helix chain 'h' and resid 112 through 147 removed outlier: 3.700A pdb=" N TRP h 127 " --> pdb=" O VAL h 123 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N CYS h 145 " --> pdb=" O GLY h 141 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE h 146 " --> pdb=" O LEU h 142 " (cutoff:3.500A) Processing helix chain 'h' and resid 148 through 150 No H-bonds generated for 'chain 'h' and resid 148 through 150' Processing helix chain 'h' and resid 156 through 167 Processing helix chain 'h' and resid 179 through 190 Processing helix chain 'h' and resid 192 through 198 removed outlier: 4.271A pdb=" N ARG h 196 " --> pdb=" O HIS h 192 " (cutoff:3.500A) Processing helix chain 'h' and resid 198 through 221 Proline residue: h 210 - end of helix Processing helix chain 'h' and resid 271 through 297 Proline residue: h 278 - end of helix removed outlier: 3.810A pdb=" N ASN h 297 " --> pdb=" O CYS h 293 " (cutoff:3.500A) Processing helix chain 'h' and resid 521 through 540 removed outlier: 3.564A pdb=" N PHE h 540 " --> pdb=" O LEU h 536 " (cutoff:3.500A) Processing helix chain 'h' and resid 558 through 573 removed outlier: 3.579A pdb=" N ILE h 562 " --> pdb=" O SER h 558 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA h 563 " --> pdb=" O SER h 559 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA h 567 " --> pdb=" O ALA h 563 " (cutoff:3.500A) Proline residue: h 568 - end of helix Processing helix chain 'h' and resid 591 through 603 removed outlier: 3.991A pdb=" N LYS h 602 " --> pdb=" O ALA h 598 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR h 603 " --> pdb=" O VAL h 599 " (cutoff:3.500A) Processing helix chain 'h' and resid 603 through 623 removed outlier: 4.442A pdb=" N THR h 607 " --> pdb=" O THR h 603 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR h 608 " --> pdb=" O ARG h 604 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA h 613 " --> pdb=" O LEU h 609 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN h 621 " --> pdb=" O VAL h 617 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS h 622 " --> pdb=" O ALA h 618 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA h 623 " --> pdb=" O ASP h 619 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 44 removed outlier: 3.748A pdb=" N MET i 37 " --> pdb=" O THR i 33 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE i 39 " --> pdb=" O GLY i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 54 Processing helix chain 'i' and resid 55 through 60 removed outlier: 3.626A pdb=" N VAL i 59 " --> pdb=" O VAL i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 62 through 80 removed outlier: 3.961A pdb=" N ALA i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 98 removed outlier: 3.883A pdb=" N LEU i 86 " --> pdb=" O THR i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 100 through 109 Processing helix chain 'i' and resid 112 through 144 removed outlier: 3.620A pdb=" N TRP i 127 " --> pdb=" O VAL i 123 " (cutoff:3.500A) Processing helix chain 'i' and resid 145 through 150 Proline residue: i 148 - end of helix No H-bonds generated for 'chain 'i' and resid 145 through 150' Processing helix chain 'i' and resid 156 through 167 removed outlier: 3.500A pdb=" N TYR i 160 " --> pdb=" O SER i 156 " (cutoff:3.500A) Processing helix chain 'i' and resid 179 through 190 Processing helix chain 'i' and resid 192 through 198 removed outlier: 4.221A pdb=" N ARG i 196 " --> pdb=" O HIS i 192 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Proline residue: i 210 - end of helix Processing helix chain 'i' and resid 271 through 297 Proline residue: i 278 - end of helix removed outlier: 3.812A pdb=" N ASN i 297 " --> pdb=" O CYS i 293 " (cutoff:3.500A) Processing helix chain 'i' and resid 521 through 540 removed outlier: 3.550A pdb=" N PHE i 540 " --> pdb=" O LEU i 536 " (cutoff:3.500A) Processing helix chain 'i' and resid 558 through 573 removed outlier: 3.845A pdb=" N ALA i 563 " --> pdb=" O SER i 559 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA i 567 " --> pdb=" O ALA i 563 " (cutoff:3.500A) Proline residue: i 568 - end of helix Processing helix chain 'i' and resid 591 through 602 removed outlier: 3.912A pdb=" N LYS i 602 " --> pdb=" O ALA i 598 " (cutoff:3.500A) Processing helix chain 'i' and resid 603 through 623 removed outlier: 4.299A pdb=" N THR i 607 " --> pdb=" O THR i 603 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR i 608 " --> pdb=" O ARG i 604 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN i 621 " --> pdb=" O VAL i 617 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS i 622 " --> pdb=" O ALA i 618 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 44 removed outlier: 3.572A pdb=" N MET j 37 " --> pdb=" O THR j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 54 Processing helix chain 'j' and resid 55 through 60 removed outlier: 3.573A pdb=" N VAL j 59 " --> pdb=" O VAL j 55 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 80 removed outlier: 3.868A pdb=" N ALA j 80 " --> pdb=" O ALA j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 98 removed outlier: 3.568A pdb=" N LEU j 86 " --> pdb=" O THR j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 109 Processing helix chain 'j' and resid 112 through 144 removed outlier: 3.690A pdb=" N TRP j 127 " --> pdb=" O VAL j 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 145 through 150 Proline residue: j 148 - end of helix No H-bonds generated for 'chain 'j' and resid 145 through 150' Processing helix chain 'j' and resid 156 through 167 removed outlier: 3.508A pdb=" N TYR j 160 " --> pdb=" O SER j 156 " (cutoff:3.500A) Processing helix chain 'j' and resid 179 through 190 Processing helix chain 'j' and resid 192 through 198 removed outlier: 4.317A pdb=" N ARG j 196 " --> pdb=" O HIS j 192 " (cutoff:3.500A) Processing helix chain 'j' and resid 198 through 221 Proline residue: j 210 - end of helix Processing helix chain 'j' and resid 271 through 297 Proline residue: j 278 - end of helix removed outlier: 3.844A pdb=" N ASN j 297 " --> pdb=" O CYS j 293 " (cutoff:3.500A) Processing helix chain 'j' and resid 521 through 541 removed outlier: 3.505A pdb=" N PHE j 540 " --> pdb=" O LEU j 536 " (cutoff:3.500A) Processing helix chain 'j' and resid 558 through 573 removed outlier: 3.600A pdb=" N ILE j 562 " --> pdb=" O SER j 558 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA j 563 " --> pdb=" O SER j 559 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA j 567 " --> pdb=" O ALA j 563 " (cutoff:3.500A) Proline residue: j 568 - end of helix Processing helix chain 'j' and resid 591 through 603 removed outlier: 3.859A pdb=" N LYS j 602 " --> pdb=" O ALA j 598 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR j 603 " --> pdb=" O VAL j 599 " (cutoff:3.500A) Processing helix chain 'j' and resid 603 through 623 removed outlier: 4.458A pdb=" N THR j 607 " --> pdb=" O THR j 603 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR j 608 " --> pdb=" O ARG j 604 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN j 621 " --> pdb=" O VAL j 617 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS j 622 " --> pdb=" O ALA j 618 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA j 623 " --> pdb=" O ASP j 619 " (cutoff:3.500A) Processing helix chain 'k' and resid 33 through 44 removed outlier: 3.607A pdb=" N MET k 37 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE k 39 " --> pdb=" O GLY k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 54 Processing helix chain 'k' and resid 55 through 60 removed outlier: 3.615A pdb=" N VAL k 59 " --> pdb=" O VAL k 55 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG k 60 " --> pdb=" O TYR k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 55 through 60' Processing helix chain 'k' and resid 62 through 80 removed outlier: 3.957A pdb=" N ALA k 80 " --> pdb=" O ALA k 76 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 98 Processing helix chain 'k' and resid 100 through 109 Processing helix chain 'k' and resid 112 through 145 removed outlier: 3.712A pdb=" N TRP k 127 " --> pdb=" O VAL k 123 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N CYS k 145 " --> pdb=" O GLY k 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 150 Processing helix chain 'k' and resid 156 through 167 Processing helix chain 'k' and resid 179 through 190 Processing helix chain 'k' and resid 192 through 198 removed outlier: 4.202A pdb=" N ARG k 196 " --> pdb=" O HIS k 192 " (cutoff:3.500A) Processing helix chain 'k' and resid 198 through 221 Proline residue: k 210 - end of helix Processing helix chain 'k' and resid 271 through 297 Proline residue: k 278 - end of helix removed outlier: 3.801A pdb=" N ASN k 297 " --> pdb=" O CYS k 293 " (cutoff:3.500A) Processing helix chain 'k' and resid 521 through 541 removed outlier: 3.570A pdb=" N PHE k 540 " --> pdb=" O LEU k 536 " (cutoff:3.500A) Processing helix chain 'k' and resid 558 through 573 removed outlier: 3.626A pdb=" N ILE k 562 " --> pdb=" O SER k 558 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA k 563 " --> pdb=" O SER k 559 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA k 567 " --> pdb=" O ALA k 563 " (cutoff:3.500A) Proline residue: k 568 - end of helix Processing helix chain 'k' and resid 591 through 602 removed outlier: 4.067A pdb=" N LYS k 602 " --> pdb=" O ALA k 598 " (cutoff:3.500A) Processing helix chain 'k' and resid 603 through 623 removed outlier: 4.343A pdb=" N THR k 607 " --> pdb=" O THR k 603 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR k 608 " --> pdb=" O ARG k 604 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN k 621 " --> pdb=" O VAL k 617 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS k 622 " --> pdb=" O ALA k 618 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA k 623 " --> pdb=" O ASP k 619 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 44 removed outlier: 4.458A pdb=" N PHE l 39 " --> pdb=" O GLY l 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG l 40 " --> pdb=" O THR l 36 " (cutoff:3.500A) Processing helix chain 'l' and resid 51 through 54 Processing helix chain 'l' and resid 55 through 60 removed outlier: 3.660A pdb=" N VAL l 59 " --> pdb=" O VAL l 55 " (cutoff:3.500A) Processing helix chain 'l' and resid 62 through 79 Processing helix chain 'l' and resid 82 through 98 Processing helix chain 'l' and resid 100 through 109 Processing helix chain 'l' and resid 112 through 147 removed outlier: 3.709A pdb=" N TRP l 127 " --> pdb=" O VAL l 123 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS l 145 " --> pdb=" O GLY l 141 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE l 146 " --> pdb=" O LEU l 142 " (cutoff:3.500A) Processing helix chain 'l' and resid 148 through 150 No H-bonds generated for 'chain 'l' and resid 148 through 150' Processing helix chain 'l' and resid 156 through 167 Processing helix chain 'l' and resid 179 through 190 Processing helix chain 'l' and resid 192 through 198 removed outlier: 4.208A pdb=" N ARG l 196 " --> pdb=" O HIS l 192 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 221 Proline residue: l 210 - end of helix Processing helix chain 'l' and resid 271 through 297 Proline residue: l 278 - end of helix removed outlier: 3.774A pdb=" N ASN l 297 " --> pdb=" O CYS l 293 " (cutoff:3.500A) Processing helix chain 'l' and resid 521 through 540 removed outlier: 3.546A pdb=" N PHE l 540 " --> pdb=" O LEU l 536 " (cutoff:3.500A) Processing helix chain 'l' and resid 558 through 573 removed outlier: 3.621A pdb=" N ILE l 562 " --> pdb=" O SER l 558 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA l 563 " --> pdb=" O SER l 559 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA l 567 " --> pdb=" O ALA l 563 " (cutoff:3.500A) Proline residue: l 568 - end of helix Processing helix chain 'l' and resid 591 through 602 removed outlier: 3.890A pdb=" N LYS l 602 " --> pdb=" O ALA l 598 " (cutoff:3.500A) Processing helix chain 'l' and resid 603 through 623 removed outlier: 4.458A pdb=" N THR l 607 " --> pdb=" O THR l 603 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR l 608 " --> pdb=" O ARG l 604 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLN l 621 " --> pdb=" O VAL l 617 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS l 622 " --> pdb=" O ALA l 618 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA l 623 " --> pdb=" O ASP l 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 26 through 29 removed outlier: 6.765A pdb=" N TRP a 241 " --> pdb=" O CYS a 254 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS a 254 " --> pdb=" O TRP a 241 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL a 243 " --> pdb=" O GLY a 252 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ARG a 251 " --> pdb=" O ARG a 174 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG a 174 " --> pdb=" O ARG a 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 495 through 498 removed outlier: 6.547A pdb=" N VAL a 301 " --> pdb=" O ILE a 496 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASP a 498 " --> pdb=" O VAL a 301 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL a 303 " --> pdb=" O ASP a 498 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN b 511 " --> pdb=" O LEU a 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 507 through 514 removed outlier: 6.029A pdb=" N VAL a 509 " --> pdb=" O GLY c 306 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY c 306 " --> pdb=" O VAL a 509 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN a 511 " --> pdb=" O LEU c 304 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL c 301 " --> pdb=" O ILE c 496 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASP c 498 " --> pdb=" O VAL c 301 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL c 303 " --> pdb=" O ASP c 498 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 542 through 545 removed outlier: 3.876A pdb=" N SER a 554 " --> pdb=" O HIS a 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 26 through 29 removed outlier: 3.632A pdb=" N ASN b 235 " --> pdb=" O ASP b 240 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP b 240 " --> pdb=" O ASN b 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 172 through 173 Processing sheet with id=AA7, first strand: chain 'b' and resid 495 through 498 removed outlier: 6.471A pdb=" N VAL b 301 " --> pdb=" O ILE b 496 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASP b 498 " --> pdb=" O VAL b 301 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL b 303 " --> pdb=" O ASP b 498 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY b 306 " --> pdb=" O VAL l 509 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL l 509 " --> pdb=" O GLY b 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 542 through 545 removed outlier: 3.763A pdb=" N SER b 554 " --> pdb=" O HIS b 545 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 26 through 29 removed outlier: 3.548A pdb=" N ASN c 235 " --> pdb=" O ASP c 240 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP c 240 " --> pdb=" O ASN c 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 223 through 224 removed outlier: 3.509A pdb=" N LEU c 255 " --> pdb=" O VAL c 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 507 through 514 removed outlier: 6.948A pdb=" N LEU d 304 " --> pdb=" O ALA c 510 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER c 512 " --> pdb=" O LYS d 302 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS d 302 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL d 301 " --> pdb=" O ILE d 496 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP d 498 " --> pdb=" O VAL d 301 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL d 303 " --> pdb=" O ASP d 498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 542 through 545 removed outlier: 3.670A pdb=" N SER c 554 " --> pdb=" O HIS c 545 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 26 through 29 removed outlier: 3.610A pdb=" N ASP d 240 " --> pdb=" O ASN d 235 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 172 through 174 Processing sheet with id=AB6, first strand: chain 'd' and resid 507 through 514 removed outlier: 5.977A pdb=" N VAL d 509 " --> pdb=" O GLY e 306 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY e 306 " --> pdb=" O VAL d 509 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL e 301 " --> pdb=" O ILE e 496 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ASP e 498 " --> pdb=" O VAL e 301 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL e 303 " --> pdb=" O ASP e 498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 542 through 545 removed outlier: 3.747A pdb=" N SER d 554 " --> pdb=" O HIS d 545 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 26 through 29 removed outlier: 3.600A pdb=" N ASN e 235 " --> pdb=" O ASP e 240 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP e 240 " --> pdb=" O ASN e 235 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 222 through 224 Processing sheet with id=AC1, first strand: chain 'e' and resid 507 through 514 removed outlier: 6.133A pdb=" N VAL e 509 " --> pdb=" O GLY f 306 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY f 306 " --> pdb=" O VAL e 509 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN e 511 " --> pdb=" O LEU f 304 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL f 301 " --> pdb=" O ILE f 496 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASP f 498 " --> pdb=" O VAL f 301 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL f 303 " --> pdb=" O ASP f 498 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 542 through 545 removed outlier: 3.716A pdb=" N SER e 554 " --> pdb=" O HIS e 545 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 26 through 29 removed outlier: 3.625A pdb=" N ASN f 235 " --> pdb=" O ASP f 240 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP f 240 " --> pdb=" O ASN f 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 222 through 224 removed outlier: 3.516A pdb=" N LEU f 255 " --> pdb=" O VAL f 170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 507 through 514 removed outlier: 5.900A pdb=" N VAL f 509 " --> pdb=" O GLY g 306 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY g 306 " --> pdb=" O VAL f 509 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL g 301 " --> pdb=" O ILE g 496 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASP g 498 " --> pdb=" O VAL g 301 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL g 303 " --> pdb=" O ASP g 498 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 542 through 545 removed outlier: 3.633A pdb=" N SER f 554 " --> pdb=" O HIS f 545 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 26 through 29 removed outlier: 3.579A pdb=" N ASN g 235 " --> pdb=" O ASP g 240 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP g 240 " --> pdb=" O ASN g 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 223 through 224 Processing sheet with id=AC9, first strand: chain 'g' and resid 507 through 514 removed outlier: 5.864A pdb=" N VAL g 509 " --> pdb=" O GLY h 306 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY h 306 " --> pdb=" O VAL g 509 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL h 301 " --> pdb=" O ILE h 496 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP h 498 " --> pdb=" O VAL h 301 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL h 303 " --> pdb=" O ASP h 498 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 542 through 545 removed outlier: 3.675A pdb=" N SER g 554 " --> pdb=" O HIS g 545 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'h' and resid 26 through 29 removed outlier: 6.885A pdb=" N TRP h 241 " --> pdb=" O CYS h 254 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N CYS h 254 " --> pdb=" O TRP h 241 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL h 243 " --> pdb=" O GLY h 252 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG h 251 " --> pdb=" O ARG h 174 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG h 174 " --> pdb=" O ARG h 251 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'h' and resid 507 through 514 removed outlier: 6.909A pdb=" N LEU i 304 " --> pdb=" O ALA h 510 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER h 512 " --> pdb=" O LYS i 302 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS i 302 " --> pdb=" O SER h 512 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL i 301 " --> pdb=" O ILE i 496 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ASP i 498 " --> pdb=" O VAL i 301 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL i 303 " --> pdb=" O ASP i 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'h' and resid 542 through 545 removed outlier: 3.828A pdb=" N SER h 554 " --> pdb=" O HIS h 545 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'i' and resid 26 through 29 Processing sheet with id=AD6, first strand: chain 'i' and resid 172 through 174 Processing sheet with id=AD7, first strand: chain 'i' and resid 507 through 514 removed outlier: 6.913A pdb=" N LEU j 304 " --> pdb=" O ALA i 510 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER i 512 " --> pdb=" O LYS j 302 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS j 302 " --> pdb=" O SER i 512 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL j 301 " --> pdb=" O ILE j 496 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASP j 498 " --> pdb=" O VAL j 301 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL j 303 " --> pdb=" O ASP j 498 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'i' and resid 542 through 545 removed outlier: 3.706A pdb=" N SER i 554 " --> pdb=" O HIS i 545 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'j' and resid 26 through 29 Processing sheet with id=AE1, first strand: chain 'j' and resid 172 through 174 Processing sheet with id=AE2, first strand: chain 'j' and resid 507 through 514 removed outlier: 6.913A pdb=" N LEU k 304 " --> pdb=" O ALA j 510 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER j 512 " --> pdb=" O LYS k 302 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS k 302 " --> pdb=" O SER j 512 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL k 301 " --> pdb=" O ILE k 496 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP k 498 " --> pdb=" O VAL k 301 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL k 303 " --> pdb=" O ASP k 498 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 542 through 545 removed outlier: 3.722A pdb=" N SER j 554 " --> pdb=" O HIS j 545 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'k' and resid 26 through 29 removed outlier: 3.570A pdb=" N ASN k 235 " --> pdb=" O ASP k 240 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP k 240 " --> pdb=" O ASN k 235 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'k' and resid 222 through 224 Processing sheet with id=AE6, first strand: chain 'k' and resid 507 through 514 removed outlier: 6.040A pdb=" N VAL k 509 " --> pdb=" O GLY l 306 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY l 306 " --> pdb=" O VAL k 509 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN k 511 " --> pdb=" O LEU l 304 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL l 301 " --> pdb=" O ILE l 496 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ASP l 498 " --> pdb=" O VAL l 301 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL l 303 " --> pdb=" O ASP l 498 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'k' and resid 542 through 545 removed outlier: 3.683A pdb=" N SER k 554 " --> pdb=" O HIS k 545 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'l' and resid 26 through 29 removed outlier: 3.612A pdb=" N ASN l 235 " --> pdb=" O ASP l 240 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP l 240 " --> pdb=" O ASN l 235 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'l' and resid 222 through 224 removed outlier: 3.529A pdb=" N LEU l 255 " --> pdb=" O VAL l 170 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'l' and resid 542 through 545 removed outlier: 3.768A pdb=" N SER l 554 " --> pdb=" O HIS l 545 " (cutoff:3.500A) 2167 hydrogen bonds defined for protein. 6393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.49 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13472 1.34 - 1.46: 6148 1.46 - 1.57: 21768 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 41520 Sorted by residual: bond pdb=" C HIS g 31 " pdb=" N PRO g 32 " ideal model delta sigma weight residual 1.334 1.348 -0.015 8.40e-03 1.42e+04 3.02e+00 bond pdb=" C HIS c 31 " pdb=" N PRO c 32 " ideal model delta sigma weight residual 1.334 1.348 -0.015 8.40e-03 1.42e+04 3.00e+00 bond pdb=" CA LEU h 47 " pdb=" CB LEU h 47 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.62e-02 3.81e+03 1.89e+00 bond pdb=" CA LEU l 47 " pdb=" CB LEU l 47 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.62e-02 3.81e+03 1.75e+00 bond pdb=" N PRO k 259 " pdb=" CA PRO k 259 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.31e-02 5.83e+03 1.24e+00 ... (remaining 41515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 56093 2.46 - 4.92: 340 4.92 - 7.38: 30 7.38 - 9.84: 1 9.84 - 12.29: 8 Bond angle restraints: 56472 Sorted by residual: angle pdb=" CA LEU k 47 " pdb=" CB LEU k 47 " pdb=" CG LEU k 47 " ideal model delta sigma weight residual 116.30 128.59 -12.29 3.50e+00 8.16e-02 1.23e+01 angle pdb=" CA LEU e 47 " pdb=" CB LEU e 47 " pdb=" CG LEU e 47 " ideal model delta sigma weight residual 116.30 128.10 -11.80 3.50e+00 8.16e-02 1.14e+01 angle pdb=" CA LEU i 47 " pdb=" CB LEU i 47 " pdb=" CG LEU i 47 " ideal model delta sigma weight residual 116.30 127.74 -11.44 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA LEU d 47 " pdb=" CB LEU d 47 " pdb=" CG LEU d 47 " ideal model delta sigma weight residual 116.30 127.67 -11.37 3.50e+00 8.16e-02 1.06e+01 angle pdb=" CA LEU g 47 " pdb=" CB LEU g 47 " pdb=" CG LEU g 47 " ideal model delta sigma weight residual 116.30 127.65 -11.35 3.50e+00 8.16e-02 1.05e+01 ... (remaining 56467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 22264 17.84 - 35.68: 1756 35.68 - 53.53: 331 53.53 - 71.37: 44 71.37 - 89.21: 49 Dihedral angle restraints: 24444 sinusoidal: 9756 harmonic: 14688 Sorted by residual: dihedral pdb=" CA GLY h 179 " pdb=" C GLY h 179 " pdb=" N GLY h 180 " pdb=" CA GLY h 180 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG j 229 " pdb=" C ARG j 229 " pdb=" N VAL j 230 " pdb=" CA VAL j 230 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG g 229 " pdb=" C ARG g 229 " pdb=" N VAL g 230 " pdb=" CA VAL g 230 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 24441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3834 0.030 - 0.059: 1516 0.059 - 0.089: 434 0.089 - 0.119: 345 0.119 - 0.149: 15 Chirality restraints: 6144 Sorted by residual: chirality pdb=" CA ASP k 506 " pdb=" N ASP k 506 " pdb=" C ASP k 506 " pdb=" CB ASP k 506 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA HIS b 31 " pdb=" N HIS b 31 " pdb=" C HIS b 31 " pdb=" CB HIS b 31 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ASP c 125 " pdb=" N ASP c 125 " pdb=" C ASP c 125 " pdb=" CB ASP c 125 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 6141 not shown) Planarity restraints: 7332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS j 31 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO j 32 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO j 32 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO j 32 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN h 100 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO h 101 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO h 101 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO h 101 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY b 209 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO b 210 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO b 210 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO b 210 " -0.021 5.00e-02 4.00e+02 ... (remaining 7329 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 21033 3.00 - 3.48: 40461 3.48 - 3.95: 60780 3.95 - 4.43: 69162 4.43 - 4.90: 114263 Nonbonded interactions: 305699 Sorted by model distance: nonbonded pdb=" O ASP k 505 " pdb=" OD1 ASP k 506 " model vdw 2.530 3.040 nonbonded pdb=" O ARG c 122 " pdb=" OD1 ASP c 125 " model vdw 2.546 3.040 nonbonded pdb=" O HIS i 31 " pdb=" OG1 THR i 36 " model vdw 2.552 3.040 nonbonded pdb=" O GLY k 179 " pdb=" OE1 GLN k 183 " model vdw 2.560 3.040 nonbonded pdb=" O LYS h 159 " pdb=" OD1 ASP h 162 " model vdw 2.570 3.040 ... (remaining 305694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.850 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 41520 Z= 0.113 Angle : 0.524 12.294 56472 Z= 0.272 Chirality : 0.040 0.149 6144 Planarity : 0.004 0.040 7332 Dihedral : 13.874 89.212 15012 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.02 % Allowed : 1.44 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.12), residues: 5004 helix: 2.15 (0.10), residues: 2664 sheet: 0.20 (0.20), residues: 576 loop : -1.46 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG h 307 TYR 0.014 0.001 TYR l 608 PHE 0.008 0.001 PHE e 157 TRP 0.012 0.001 TRP g 262 HIS 0.008 0.001 HIS l 622 Details of bonding type rmsd covalent geometry : bond 0.00226 (41520) covalent geometry : angle 0.52412 (56472) hydrogen bonds : bond 0.16385 ( 2167) hydrogen bonds : angle 5.79128 ( 6393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 716 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 37 MET cc_start: 0.8563 (tpp) cc_final: 0.8333 (mmm) REVERT: b 183 GLN cc_start: 0.7857 (mp10) cc_final: 0.7395 (mp10) REVERT: b 192 HIS cc_start: 0.7305 (t-90) cc_final: 0.6896 (t-90) REVERT: b 231 TYR cc_start: 0.7652 (m-80) cc_final: 0.7414 (m-10) REVERT: b 592 GLU cc_start: 0.8333 (tp30) cc_final: 0.8090 (tm-30) REVERT: b 615 LEU cc_start: 0.9049 (mt) cc_final: 0.8598 (mt) REVERT: c 183 GLN cc_start: 0.8061 (mp10) cc_final: 0.7768 (mp10) REVERT: d 183 GLN cc_start: 0.8182 (mp10) cc_final: 0.7487 (mp10) REVERT: d 593 GLU cc_start: 0.8483 (tp30) cc_final: 0.8224 (tp30) REVERT: e 183 GLN cc_start: 0.8028 (mp10) cc_final: 0.7823 (mp10) REVERT: e 593 GLU cc_start: 0.8544 (tp30) cc_final: 0.8267 (tp30) REVERT: f 183 GLN cc_start: 0.7887 (mp10) cc_final: 0.7432 (mp10) REVERT: g 192 HIS cc_start: 0.7282 (t-90) cc_final: 0.6889 (t70) REVERT: h 136 LEU cc_start: 0.8048 (tt) cc_final: 0.7775 (tp) REVERT: h 592 GLU cc_start: 0.8322 (tp30) cc_final: 0.8097 (tm-30) REVERT: i 125 ASP cc_start: 0.7929 (t0) cc_final: 0.7579 (t0) REVERT: i 128 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7927 (ttp-110) REVERT: i 183 GLN cc_start: 0.7987 (mp10) cc_final: 0.7682 (mp10) REVERT: j 593 GLU cc_start: 0.8290 (tp30) cc_final: 0.7967 (tp30) outliers start: 1 outliers final: 0 residues processed: 716 average time/residue: 0.2752 time to fit residues: 306.6406 Evaluate side-chains 564 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.5980 chunk 470 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 606 GLN ** d 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 235 ASN f 236 HIS ** f 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 622 HIS j 235 ASN ** j 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 236 HIS ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.178756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141583 restraints weight = 48657.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139269 restraints weight = 64745.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140487 restraints weight = 67090.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140449 restraints weight = 45200.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140974 restraints weight = 43895.826| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 41520 Z= 0.218 Angle : 0.634 11.637 56472 Z= 0.328 Chirality : 0.044 0.173 6144 Planarity : 0.005 0.045 7332 Dihedral : 4.499 21.161 5700 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.01 % Allowed : 8.66 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.12), residues: 5004 helix: 1.90 (0.10), residues: 2820 sheet: 0.84 (0.24), residues: 444 loop : -1.58 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 207 TYR 0.021 0.002 TYR g 608 PHE 0.016 0.001 PHE b 188 TRP 0.015 0.002 TRP i 532 HIS 0.013 0.001 HIS j 236 Details of bonding type rmsd covalent geometry : bond 0.00543 (41520) covalent geometry : angle 0.63448 (56472) hydrogen bonds : bond 0.05471 ( 2167) hydrogen bonds : angle 4.54231 ( 6393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 573 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 75 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7805 (t-90) REVERT: b 75 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7837 (t-90) REVERT: b 183 GLN cc_start: 0.7715 (mp10) cc_final: 0.7288 (mp10) REVERT: b 192 HIS cc_start: 0.7091 (t-90) cc_final: 0.6865 (t-90) REVERT: b 231 TYR cc_start: 0.7759 (m-80) cc_final: 0.7473 (m-10) REVERT: b 592 GLU cc_start: 0.8378 (tp30) cc_final: 0.8120 (tm-30) REVERT: c 183 GLN cc_start: 0.7839 (mp10) cc_final: 0.7518 (mp10) REVERT: d 83 TYR cc_start: 0.7916 (t80) cc_final: 0.7714 (t80) REVERT: e 75 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7937 (t-90) REVERT: e 593 GLU cc_start: 0.8255 (tp30) cc_final: 0.8022 (tp30) REVERT: g 75 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7769 (t-90) REVERT: g 183 GLN cc_start: 0.7474 (mt0) cc_final: 0.7139 (mp10) REVERT: g 307 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6832 (ttm-80) REVERT: h 75 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7848 (t-90) REVERT: h 136 LEU cc_start: 0.7826 (tt) cc_final: 0.6953 (tt) REVERT: h 602 LYS cc_start: 0.8669 (ptmt) cc_final: 0.7276 (ttmt) REVERT: i 125 ASP cc_start: 0.7289 (t0) cc_final: 0.6735 (t0) REVERT: i 183 GLN cc_start: 0.7855 (mp10) cc_final: 0.7381 (mp10) REVERT: k 183 GLN cc_start: 0.7773 (mp10) cc_final: 0.7517 (mp10) REVERT: k 501 LYS cc_start: 0.8342 (ptpt) cc_final: 0.8127 (ptpt) outliers start: 85 outliers final: 68 residues processed: 613 average time/residue: 0.2509 time to fit residues: 238.5618 Evaluate side-chains 611 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 538 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 584 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 178 GLU Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 584 THR Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 33 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 602 LYS Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 543 LEU Chi-restraints excluded: chain e residue 584 THR Chi-restraints excluded: chain e residue 615 LEU Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 178 GLU Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 499 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 499 VAL Chi-restraints excluded: chain g residue 615 LEU Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 615 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 615 LEU Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 126 THR Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 238 ARG Chi-restraints excluded: chain j residue 499 VAL Chi-restraints excluded: chain j residue 615 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 584 THR Chi-restraints excluded: chain k residue 615 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 584 THR Chi-restraints excluded: chain l residue 615 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 478 optimal weight: 2.9990 chunk 403 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 264 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 606 GLN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.180617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144922 restraints weight = 48397.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143326 restraints weight = 60672.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143950 restraints weight = 65137.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143854 restraints weight = 43422.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144315 restraints weight = 42227.149| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 41520 Z= 0.140 Angle : 0.558 11.798 56472 Z= 0.286 Chirality : 0.041 0.166 6144 Planarity : 0.004 0.045 7332 Dihedral : 4.326 21.197 5700 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.23 % Allowed : 11.58 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.12), residues: 5004 helix: 2.08 (0.10), residues: 2844 sheet: 0.72 (0.24), residues: 468 loop : -1.53 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG j 207 TYR 0.018 0.001 TYR a 160 PHE 0.016 0.001 PHE l 188 TRP 0.012 0.001 TRP l 532 HIS 0.007 0.001 HIS l 236 Details of bonding type rmsd covalent geometry : bond 0.00329 (41520) covalent geometry : angle 0.55831 (56472) hydrogen bonds : bond 0.04588 ( 2167) hydrogen bonds : angle 4.27914 ( 6393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 568 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 75 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: b 75 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7900 (t-90) REVERT: b 136 LEU cc_start: 0.8169 (tp) cc_final: 0.7962 (tp) REVERT: b 183 GLN cc_start: 0.7586 (mp10) cc_final: 0.7294 (mp10) REVERT: b 231 TYR cc_start: 0.7696 (m-80) cc_final: 0.7400 (m-10) REVERT: b 593 GLU cc_start: 0.7725 (tp30) cc_final: 0.7406 (tp30) REVERT: c 47 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8075 (pp) REVERT: d 83 TYR cc_start: 0.7946 (t80) cc_final: 0.7312 (t80) REVERT: e 75 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7980 (t-90) REVERT: e 237 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7674 (mtp-110) REVERT: g 75 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: g 183 GLN cc_start: 0.7426 (mt0) cc_final: 0.7060 (mp10) REVERT: h 47 LEU cc_start: 0.8241 (pp) cc_final: 0.8005 (pp) REVERT: h 75 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7796 (t-90) REVERT: h 136 LEU cc_start: 0.7528 (tt) cc_final: 0.7133 (tt) REVERT: i 606 GLN cc_start: 0.7775 (tp40) cc_final: 0.7556 (tp40) REVERT: j 75 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7880 (t-90) REVERT: k 75 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7636 (t-90) REVERT: k 502 SER cc_start: 0.8239 (m) cc_final: 0.7957 (p) REVERT: k 599 VAL cc_start: 0.8266 (p) cc_final: 0.8042 (p) outliers start: 94 outliers final: 63 residues processed: 610 average time/residue: 0.2454 time to fit residues: 232.9116 Evaluate side-chains 610 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 539 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain a residue 615 LEU Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain b residue 615 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 178 GLU Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 33 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 142 LEU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 182 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 615 LEU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 178 GLU Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 499 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 499 VAL Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain g residue 615 LEU Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 496 ILE Chi-restraints excluded: chain h residue 615 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 615 LEU Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 107 ARG Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 238 ARG Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 543 LEU Chi-restraints excluded: chain j residue 615 LEU Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 615 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 143 VAL Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 304 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 486 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 462 optimal weight: 10.0000 chunk 435 optimal weight: 0.1980 chunk 220 optimal weight: 1.9990 chunk 461 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 606 GLN ** d 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 46 GLN ** e 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.179607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143773 restraints weight = 48372.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.142078 restraints weight = 59570.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142941 restraints weight = 62666.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142786 restraints weight = 43341.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143255 restraints weight = 42457.588| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41520 Z= 0.162 Angle : 0.573 11.823 56472 Z= 0.293 Chirality : 0.042 0.162 6144 Planarity : 0.004 0.045 7332 Dihedral : 4.277 22.100 5700 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.10 % Allowed : 12.76 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.12), residues: 5004 helix: 2.12 (0.10), residues: 2844 sheet: 0.66 (0.24), residues: 480 loop : -1.53 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG j 207 TYR 0.021 0.001 TYR e 160 PHE 0.014 0.001 PHE l 600 TRP 0.013 0.001 TRP l 532 HIS 0.009 0.001 HIS a 622 Details of bonding type rmsd covalent geometry : bond 0.00395 (41520) covalent geometry : angle 0.57259 (56472) hydrogen bonds : bond 0.04586 ( 2167) hydrogen bonds : angle 4.19862 ( 6393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 564 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 75 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7805 (t-90) REVERT: b 75 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7800 (t-90) REVERT: c 47 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8124 (pp) REVERT: d 83 TYR cc_start: 0.7995 (t80) cc_final: 0.7451 (t80) REVERT: d 207 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7404 (mpp80) REVERT: e 237 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7698 (mtp-110) REVERT: g 75 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7901 (t-90) REVERT: h 75 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7776 (t-90) REVERT: i 47 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8263 (pp) REVERT: i 606 GLN cc_start: 0.7893 (tp40) cc_final: 0.7591 (tp40) REVERT: j 75 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7929 (t-90) REVERT: k 75 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: k 502 SER cc_start: 0.8276 (m) cc_final: 0.8007 (p) REVERT: l 183 GLN cc_start: 0.7531 (mp10) cc_final: 0.7194 (mp10) outliers start: 131 outliers final: 90 residues processed: 637 average time/residue: 0.2426 time to fit residues: 241.0780 Evaluate side-chains 643 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 545 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 253 GLU Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain b residue 615 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 178 GLU Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 33 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 142 LEU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 182 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 183 GLN Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 543 LEU Chi-restraints excluded: chain e residue 615 LEU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 292 VAL Chi-restraints excluded: chain f residue 499 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain g residue 499 VAL Chi-restraints excluded: chain g residue 503 MET Chi-restraints excluded: chain g residue 615 LEU Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain h residue 496 ILE Chi-restraints excluded: chain h residue 586 SER Chi-restraints excluded: chain h residue 602 LYS Chi-restraints excluded: chain h residue 615 LEU Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 292 VAL Chi-restraints excluded: chain i residue 503 MET Chi-restraints excluded: chain i residue 543 LEU Chi-restraints excluded: chain i residue 615 LEU Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 107 ARG Chi-restraints excluded: chain j residue 126 THR Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 238 ARG Chi-restraints excluded: chain j residue 292 VAL Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 543 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 292 VAL Chi-restraints excluded: chain k residue 615 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 143 VAL Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 242 optimal weight: 0.0020 chunk 296 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 233 optimal weight: 0.0050 chunk 226 optimal weight: 0.2980 chunk 146 optimal weight: 0.9990 chunk 305 optimal weight: 6.9990 chunk 303 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 140 HIS a 622 HIS c 93 HIS c 622 HIS d 622 HIS e 622 HIS ** g 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.173167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.145094 restraints weight = 47568.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143203 restraints weight = 94362.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143568 restraints weight = 90306.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142937 restraints weight = 66801.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143269 restraints weight = 64724.845| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41520 Z= 0.103 Angle : 0.523 12.122 56472 Z= 0.265 Chirality : 0.039 0.152 6144 Planarity : 0.004 0.046 7332 Dihedral : 4.039 23.435 5700 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.75 % Allowed : 14.42 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.12), residues: 5004 helix: 2.35 (0.10), residues: 2832 sheet: 0.87 (0.24), residues: 480 loop : -1.50 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 307 TYR 0.016 0.001 TYR e 160 PHE 0.010 0.001 PHE l 600 TRP 0.010 0.001 TRP l 532 HIS 0.007 0.001 HIS f 236 Details of bonding type rmsd covalent geometry : bond 0.00215 (41520) covalent geometry : angle 0.52311 (56472) hydrogen bonds : bond 0.03587 ( 2167) hydrogen bonds : angle 3.99926 ( 6393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 582 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 75 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7740 (t-90) REVERT: b 75 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7719 (t-90) REVERT: c 47 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7968 (pp) REVERT: d 83 TYR cc_start: 0.7954 (t80) cc_final: 0.7630 (t80) REVERT: e 237 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7529 (mtp-110) REVERT: g 47 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8097 (pp) REVERT: g 75 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7745 (t-90) REVERT: h 75 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7726 (t-90) REVERT: i 47 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8192 (pp) REVERT: i 160 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8260 (t80) REVERT: i 183 GLN cc_start: 0.7136 (mp10) cc_final: 0.6928 (mp10) REVERT: j 75 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7819 (t-90) REVERT: k 75 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7550 (t-90) REVERT: k 502 SER cc_start: 0.8127 (m) cc_final: 0.7924 (p) outliers start: 74 outliers final: 38 residues processed: 621 average time/residue: 0.2784 time to fit residues: 265.8061 Evaluate side-chains 594 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 546 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 142 LEU Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain f residue 30 VAL Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 503 MET Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 602 LYS Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 TYR Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 503 MET Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 107 ARG Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 5.9990 chunk 371 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 419 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 486 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 247 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 236 HIS h 297 ASN i 606 GLN k 297 ASN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.177821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142087 restraints weight = 48919.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139024 restraints weight = 88296.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140239 restraints weight = 88519.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140357 restraints weight = 54619.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142024 restraints weight = 49401.842| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 41520 Z= 0.238 Angle : 0.648 12.673 56472 Z= 0.329 Chirality : 0.044 0.175 6144 Planarity : 0.005 0.066 7332 Dihedral : 4.356 22.690 5700 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.01 % Allowed : 14.87 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.12), residues: 5004 helix: 2.09 (0.10), residues: 2844 sheet: 0.91 (0.25), residues: 456 loop : -1.58 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG j 207 TYR 0.024 0.002 TYR g 608 PHE 0.022 0.002 PHE c 600 TRP 0.014 0.002 TRP l 532 HIS 0.015 0.001 HIS b 31 Details of bonding type rmsd covalent geometry : bond 0.00600 (41520) covalent geometry : angle 0.64835 (56472) hydrogen bonds : bond 0.05264 ( 2167) hydrogen bonds : angle 4.21896 ( 6393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 565 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 75 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7901 (t-90) REVERT: a 244 ARG cc_start: 0.6870 (ptp90) cc_final: 0.6657 (ttm110) REVERT: b 75 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7933 (t-90) REVERT: c 47 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8080 (pp) REVERT: c 183 GLN cc_start: 0.7665 (mp10) cc_final: 0.7171 (mp10) REVERT: d 207 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7416 (mpp80) REVERT: e 237 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7830 (mtp-110) REVERT: e 251 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7587 (mtt90) REVERT: g 75 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.8048 (t-90) REVERT: h 75 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: i 47 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8337 (pp) REVERT: i 160 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8393 (t80) REVERT: i 496 ILE cc_start: 0.8527 (mt) cc_final: 0.8293 (mt) REVERT: j 192 HIS cc_start: 0.7772 (t-90) cc_final: 0.7262 (t-90) REVERT: k 75 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7738 (t-90) REVERT: k 189 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8207 (tt) REVERT: k 502 SER cc_start: 0.8369 (m) cc_final: 0.8114 (p) REVERT: l 183 GLN cc_start: 0.7879 (mp10) cc_final: 0.7353 (mp10) outliers start: 127 outliers final: 93 residues processed: 640 average time/residue: 0.2637 time to fit residues: 260.7035 Evaluate side-chains 640 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 538 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 501 LYS Chi-restraints excluded: chain a residue 584 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 230 VAL Chi-restraints excluded: chain b residue 253 GLU Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 503 MET Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 584 THR Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 126 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 182 THR Chi-restraints excluded: chain d residue 230 VAL Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 602 LYS Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 615 LEU Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 292 VAL Chi-restraints excluded: chain f residue 499 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain g residue 499 VAL Chi-restraints excluded: chain g residue 615 LEU Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 496 ILE Chi-restraints excluded: chain h residue 586 SER Chi-restraints excluded: chain h residue 602 LYS Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 TYR Chi-restraints excluded: chain i residue 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 292 VAL Chi-restraints excluded: chain i residue 615 LEU Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 126 THR Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 238 ARG Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 499 VAL Chi-restraints excluded: chain j residue 503 MET Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 189 LEU Chi-restraints excluded: chain k residue 292 VAL Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 136 LEU Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 292 VAL Chi-restraints excluded: chain l residue 499 VAL Chi-restraints excluded: chain l residue 584 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 267 optimal weight: 0.9990 chunk 367 optimal weight: 3.9990 chunk 337 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 384 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 471 optimal weight: 2.9990 chunk 413 optimal weight: 2.9990 chunk 323 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 606 GLN h 57 ASN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.181504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143729 restraints weight = 48196.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140654 restraints weight = 84599.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142370 restraints weight = 80521.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142297 restraints weight = 50433.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142863 restraints weight = 49849.539| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41520 Z= 0.126 Angle : 0.559 12.621 56472 Z= 0.282 Chirality : 0.041 0.165 6144 Planarity : 0.004 0.047 7332 Dihedral : 4.163 22.873 5700 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.04 % Allowed : 16.24 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.12), residues: 5004 helix: 2.30 (0.10), residues: 2832 sheet: 0.74 (0.24), residues: 480 loop : -1.58 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG h 207 TYR 0.019 0.001 TYR g 608 PHE 0.020 0.001 PHE c 600 TRP 0.013 0.001 TRP l 532 HIS 0.007 0.001 HIS b 31 Details of bonding type rmsd covalent geometry : bond 0.00296 (41520) covalent geometry : angle 0.55919 (56472) hydrogen bonds : bond 0.04020 ( 2167) hydrogen bonds : angle 4.03359 ( 6393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 550 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 75 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7963 (t-90) REVERT: b 75 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7929 (t-90) REVERT: c 47 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8042 (pp) REVERT: c 183 GLN cc_start: 0.7508 (mp10) cc_final: 0.7210 (mp10) REVERT: d 83 TYR cc_start: 0.7907 (t80) cc_final: 0.7469 (t80) REVERT: e 237 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7756 (mtp-110) REVERT: e 251 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7529 (mtt90) REVERT: g 75 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.8010 (t-90) REVERT: h 75 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7931 (t-90) REVERT: i 47 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8235 (pp) REVERT: i 160 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8449 (t80) REVERT: i 183 GLN cc_start: 0.7682 (mp10) cc_final: 0.7177 (mp10) REVERT: j 192 HIS cc_start: 0.7675 (t-90) cc_final: 0.7445 (t-90) REVERT: k 75 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7714 (t-90) REVERT: k 189 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8096 (tt) REVERT: l 183 GLN cc_start: 0.7656 (mp10) cc_final: 0.7161 (mp10) outliers start: 86 outliers final: 68 residues processed: 600 average time/residue: 0.2975 time to fit residues: 275.8150 Evaluate side-chains 619 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 542 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 501 LYS Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 182 THR Chi-restraints excluded: chain d residue 230 VAL Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 602 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 503 MET Chi-restraints excluded: chain e residue 615 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 503 MET Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain h residue 602 LYS Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 TYR Chi-restraints excluded: chain i residue 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 503 MET Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 107 ARG Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 238 ARG Chi-restraints excluded: chain j residue 292 VAL Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 499 VAL Chi-restraints excluded: chain j residue 543 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 189 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 146 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 417 optimal weight: 4.9990 chunk 483 optimal weight: 1.9990 chunk 353 optimal weight: 0.0670 chunk 25 optimal weight: 0.3980 chunk 201 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 606 GLN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.186749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156387 restraints weight = 47315.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154429 restraints weight = 85390.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154882 restraints weight = 91321.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154871 restraints weight = 54992.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.156368 restraints weight = 47110.333| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 41520 Z= 0.110 Angle : 0.545 12.524 56472 Z= 0.273 Chirality : 0.040 0.176 6144 Planarity : 0.004 0.052 7332 Dihedral : 4.001 22.251 5700 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.92 % Allowed : 16.43 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.12), residues: 5004 helix: 2.39 (0.10), residues: 2832 sheet: 0.84 (0.24), residues: 480 loop : -1.55 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG a 307 TYR 0.016 0.001 TYR g 608 PHE 0.018 0.001 PHE c 600 TRP 0.011 0.001 TRP l 532 HIS 0.006 0.001 HIS f 236 Details of bonding type rmsd covalent geometry : bond 0.00247 (41520) covalent geometry : angle 0.54487 (56472) hydrogen bonds : bond 0.03616 ( 2167) hydrogen bonds : angle 3.92343 ( 6393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 559 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 75 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7815 (t-90) REVERT: b 207 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7093 (mtt90) REVERT: c 47 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7876 (pp) REVERT: c 183 GLN cc_start: 0.7426 (mt0) cc_final: 0.7151 (mp10) REVERT: d 75 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7557 (t-90) REVERT: d 83 TYR cc_start: 0.7913 (t80) cc_final: 0.7520 (t80) REVERT: e 237 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7529 (mtp-110) REVERT: e 251 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7411 (mtt90) REVERT: g 47 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8099 (pp) REVERT: g 75 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7847 (t-90) REVERT: h 75 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7791 (t-90) REVERT: i 47 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8206 (pp) REVERT: i 160 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8358 (t80) REVERT: i 183 GLN cc_start: 0.7548 (mp10) cc_final: 0.6993 (mp10) REVERT: i 496 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8156 (mt) REVERT: k 75 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7543 (t-90) REVERT: k 189 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7995 (tt) REVERT: l 183 GLN cc_start: 0.7431 (mp10) cc_final: 0.7091 (mp10) outliers start: 81 outliers final: 60 residues processed: 606 average time/residue: 0.2855 time to fit residues: 267.7656 Evaluate side-chains 618 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 547 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 501 LYS Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 69 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 182 THR Chi-restraints excluded: chain d residue 230 VAL Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 602 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain f residue 30 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 606 GLN Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 503 MET Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 TYR Chi-restraints excluded: chain i residue 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain i residue 503 MET Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 292 VAL Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 499 VAL Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 189 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 136 LEU Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 364 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 466 optimal weight: 0.5980 chunk 236 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 236 HIS ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.169760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132125 restraints weight = 47959.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130717 restraints weight = 79993.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131482 restraints weight = 93050.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132093 restraints weight = 52112.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133660 restraints weight = 44110.317| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41520 Z= 0.149 Angle : 0.578 12.776 56472 Z= 0.289 Chirality : 0.041 0.167 6144 Planarity : 0.004 0.055 7332 Dihedral : 4.044 21.064 5700 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.04 % Allowed : 16.67 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.12), residues: 5004 helix: 2.36 (0.10), residues: 2832 sheet: 0.78 (0.24), residues: 480 loop : -1.59 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG j 207 TYR 0.019 0.001 TYR e 160 PHE 0.018 0.001 PHE c 600 TRP 0.011 0.001 TRP l 532 HIS 0.009 0.001 HIS b 31 Details of bonding type rmsd covalent geometry : bond 0.00363 (41520) covalent geometry : angle 0.57750 (56472) hydrogen bonds : bond 0.04101 ( 2167) hydrogen bonds : angle 3.95898 ( 6393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 555 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 75 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7895 (t-90) REVERT: c 47 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7927 (pp) REVERT: c 160 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8319 (t80) REVERT: c 183 GLN cc_start: 0.7533 (mt0) cc_final: 0.7198 (mp10) REVERT: d 75 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7705 (t-90) REVERT: d 83 TYR cc_start: 0.7902 (t80) cc_final: 0.7524 (t80) REVERT: e 237 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7765 (mtp-110) REVERT: e 251 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7533 (mtt90) REVERT: g 75 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7976 (t-90) REVERT: h 75 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7896 (t-90) REVERT: h 597 ASP cc_start: 0.8184 (t0) cc_final: 0.7979 (t0) REVERT: i 47 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8247 (pp) REVERT: i 160 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8348 (t80) REVERT: i 183 GLN cc_start: 0.7658 (mp10) cc_final: 0.7052 (mp10) REVERT: i 496 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8188 (mt) REVERT: j 160 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8278 (t80) REVERT: j 237 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7699 (mtp-110) REVERT: k 75 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7697 (t-90) REVERT: k 189 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8048 (tt) REVERT: l 160 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8325 (t80) REVERT: l 183 GLN cc_start: 0.7603 (mp10) cc_final: 0.7118 (mp10) outliers start: 86 outliers final: 69 residues processed: 606 average time/residue: 0.2983 time to fit residues: 279.0064 Evaluate side-chains 622 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 540 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 501 LYS Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 69 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 160 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 182 THR Chi-restraints excluded: chain d residue 230 VAL Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 602 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain f residue 30 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 230 VAL Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 TYR Chi-restraints excluded: chain i residue 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain i residue 503 MET Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 160 TYR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 292 VAL Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 496 ILE Chi-restraints excluded: chain j residue 499 VAL Chi-restraints excluded: chain j residue 503 MET Chi-restraints excluded: chain j residue 543 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 189 LEU Chi-restraints excluded: chain k residue 602 LYS Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 136 LEU Chi-restraints excluded: chain l residue 160 TYR Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 356 optimal weight: 4.9990 chunk 322 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 444 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 326 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 606 GLN f 606 GLN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.185518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153991 restraints weight = 47490.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151904 restraints weight = 88766.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152665 restraints weight = 93370.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152490 restraints weight = 57322.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.153946 restraints weight = 49968.781| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41520 Z= 0.115 Angle : 0.554 12.990 56472 Z= 0.277 Chirality : 0.040 0.181 6144 Planarity : 0.004 0.055 7332 Dihedral : 3.945 21.120 5700 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.01 % Allowed : 16.88 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.12), residues: 5004 helix: 2.43 (0.10), residues: 2832 sheet: 0.85 (0.24), residues: 480 loop : -1.56 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG j 207 TYR 0.016 0.001 TYR e 160 PHE 0.017 0.001 PHE c 600 TRP 0.014 0.001 TRP i 262 HIS 0.010 0.001 HIS i 236 Details of bonding type rmsd covalent geometry : bond 0.00265 (41520) covalent geometry : angle 0.55435 (56472) hydrogen bonds : bond 0.03585 ( 2167) hydrogen bonds : angle 3.87136 ( 6393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 560 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 75 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7840 (t-90) REVERT: b 207 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7099 (mtt90) REVERT: c 47 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7838 (pp) REVERT: c 160 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8315 (t80) REVERT: c 183 GLN cc_start: 0.7391 (mt0) cc_final: 0.6933 (mp10) REVERT: d 75 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: d 83 TYR cc_start: 0.7956 (t80) cc_final: 0.7623 (t80) REVERT: e 237 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7541 (mtp-110) REVERT: e 251 ARG cc_start: 0.7645 (mmm-85) cc_final: 0.7417 (mtt90) REVERT: g 47 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8169 (pp) REVERT: h 75 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7832 (t-90) REVERT: i 47 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8195 (pp) REVERT: i 160 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8403 (t80) REVERT: i 183 GLN cc_start: 0.7539 (mp10) cc_final: 0.6971 (mp10) REVERT: i 496 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8131 (mt) REVERT: j 160 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8248 (t80) REVERT: k 75 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7674 (t-90) REVERT: k 189 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7940 (tt) REVERT: l 160 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8377 (t80) REVERT: l 183 GLN cc_start: 0.7394 (mp10) cc_final: 0.7005 (mp10) outliers start: 85 outliers final: 64 residues processed: 610 average time/residue: 0.3032 time to fit residues: 285.5409 Evaluate side-chains 625 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 548 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 501 LYS Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain b residue 543 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 69 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 160 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 182 THR Chi-restraints excluded: chain d residue 230 VAL Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 143 VAL Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 503 MET Chi-restraints excluded: chain f residue 30 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 230 VAL Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 160 TYR Chi-restraints excluded: chain i residue 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain i residue 503 MET Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 160 TYR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 292 VAL Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 499 VAL Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 143 VAL Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 189 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 136 LEU Chi-restraints excluded: chain l residue 160 TYR Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain l residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 304 optimal weight: 7.9990 chunk 394 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 471 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 392 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 431 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.195420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159827 restraints weight = 48836.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160684 restraints weight = 91544.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160512 restraints weight = 72416.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.160786 restraints weight = 39136.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163327 restraints weight = 32512.664| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 41520 Z= 0.268 Angle : 0.687 13.461 56472 Z= 0.349 Chirality : 0.046 0.179 6144 Planarity : 0.005 0.058 7332 Dihedral : 4.410 24.040 5700 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.11 % Allowed : 16.93 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.12), residues: 5004 helix: 2.12 (0.10), residues: 2832 sheet: 0.82 (0.25), residues: 456 loop : -1.69 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG g 307 TYR 0.024 0.002 TYR e 160 PHE 0.021 0.002 PHE d 188 TRP 0.014 0.002 TRP l 532 HIS 0.016 0.002 HIS h 31 Details of bonding type rmsd covalent geometry : bond 0.00674 (41520) covalent geometry : angle 0.68690 (56472) hydrogen bonds : bond 0.05494 ( 2167) hydrogen bonds : angle 4.19871 ( 6393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6404.99 seconds wall clock time: 111 minutes 18.17 seconds (6678.17 seconds total)