Starting phenix.real_space_refine on Sun Feb 8 03:28:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9op5_70679/02_2026/9op5_70679.cif Found real_map, /net/cci-nas-00/data/ceres_data/9op5_70679/02_2026/9op5_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_70679/02_2026/9op5_70679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9op5_70679/02_2026/9op5_70679.map" model { file = "/net/cci-nas-00/data/ceres_data/9op5_70679/02_2026/9op5_70679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9op5_70679/02_2026/9op5_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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: 9.24, per 1000 atoms: 0.23 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: 3.47 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.60 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: 8.19 Time building geometry restraints manager: 4.59 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.490 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: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 36.870 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.170 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- 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 are 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 : 1.614 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: 0.7651 (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: 0.2951 time to fit residues: 328.8125 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 : 1.505 ------------------------------------------------------------------------------- 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 are 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 : 1.458 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: 0.7772 (mp10) cc_final: 0.7517 (mp10) REVERT: k 501 LYS cc_start: 0.8343 (ptpt) cc_final: 0.8127 (ptpt) outliers start: 85 outliers final: 68 residues processed: 613 average time/residue: 0.2994 time to fit residues: 283.5551 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 : 1.634 ------------------------------------------------------------------------------- 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 are 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 : 1.680 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: 0.7963 (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: e 592 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7873 (tm-30) 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: 0.8006 (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: 0.8081 (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: 0.2989 time to fit residues: 283.2314 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 : 1.604 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.180519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143518 restraints weight = 48426.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140593 restraints weight = 79570.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141888 restraints weight = 82876.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142164 restraints weight = 48924.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.144259 restraints weight = 43838.136| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41520 Z= 0.161 Angle : 0.571 11.861 56472 Z= 0.292 Chirality : 0.042 0.162 6144 Planarity : 0.004 0.045 7332 Dihedral : 4.279 21.968 5700 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.03 % Allowed : 12.74 % Favored : 84.23 % 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 are not related in a simple way. whole: 1.22 (0.12), residues: 5004 helix: 2.12 (0.10), residues: 2844 sheet: 0.65 (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 0.013 0.001 PHE l 600 TRP 0.013 0.001 TRP l 532 HIS 0.008 0.001 HIS g 31 Details of bonding type rmsd covalent geometry : bond 0.00394 (41520) covalent geometry : angle 0.57090 (56472) hydrogen bonds : bond 0.04584 ( 2167) hydrogen bonds : angle 4.20388 ( 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 691 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 563 time to evaluate : 1.546 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: symmetry clash REVERT: a 75 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7797 (t-90) REVERT: b 75 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7792 (t-90) REVERT: c 47 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8123 (pp) REVERT: d 83 TYR cc_start: 0.7963 (t80) cc_final: 0.7382 (t80) REVERT: d 207 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7150 (mpp80) REVERT: e 75 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.8028 (t-90) REVERT: e 237 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7726 (mtp-110) REVERT: e 592 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7896 (tm-30) REVERT: g 75 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7893 (t-90) REVERT: g 192 HIS cc_start: 0.7515 (t70) cc_final: 0.7286 (t-90) REVERT: h 75 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7762 (t-90) REVERT: i 47 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8185 (pp) REVERT: i 606 GLN cc_start: 0.8000 (tp40) cc_final: 0.7653 (tp40) REVERT: j 75 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7889 (t-90) REVERT: k 75 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7692 (t-90) REVERT: k 502 SER cc_start: 0.8322 (m) cc_final: 0.8028 (p) REVERT: l 183 GLN cc_start: 0.7651 (mp10) cc_final: 0.7124 (mp10) outliers start: 128 outliers final: 89 residues processed: 635 average time/residue: 0.2955 time to fit residues: 291.2121 Evaluate side-chains 645 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 547 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 75 HIS 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 543 LEU 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 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 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 242 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 226 optimal weight: 0.3980 chunk 146 optimal weight: 0.8980 chunk 305 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 283 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 622 HIS c 93 HIS c 622 HIS d 622 HIS e 622 HIS f 236 HIS ** g 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 606 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.182746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143811 restraints weight = 48147.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140985 restraints weight = 76094.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142865 restraints weight = 73031.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142661 restraints weight = 45640.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143304 restraints weight = 42874.151| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41520 Z= 0.115 Angle : 0.535 12.085 56472 Z= 0.272 Chirality : 0.040 0.162 6144 Planarity : 0.004 0.051 7332 Dihedral : 4.110 21.393 5700 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.32 % Allowed : 14.02 % Favored : 83.66 % 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 are not related in a simple way. whole: 1.40 (0.12), residues: 5004 helix: 2.30 (0.10), residues: 2832 sheet: 0.81 (0.24), residues: 480 loop : -1.52 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 307 TYR 0.017 0.001 TYR e 160 PHE 0.011 0.001 PHE l 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 0.00260 (41520) covalent geometry : angle 0.53512 (56472) hydrogen bonds : bond 0.03889 ( 2167) hydrogen bonds : angle 4.05666 ( 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 664 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 566 time to evaluate : 1.642 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: a 75 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7901 (t-90) REVERT: b 75 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7870 (t-90) REVERT: c 47 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8036 (pp) REVERT: d 83 TYR cc_start: 0.7915 (t80) cc_final: 0.7420 (t80) REVERT: d 183 GLN cc_start: 0.7612 (mp10) cc_final: 0.7234 (mp10) REVERT: e 237 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7772 (mtp-110) REVERT: e 592 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7890 (tm-30) REVERT: g 75 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7907 (t-90) REVERT: h 75 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7844 (t-90) REVERT: i 47 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8186 (pp) REVERT: i 160 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8364 (t80) REVERT: i 183 GLN cc_start: 0.7524 (mp10) cc_final: 0.7111 (mp10) REVERT: j 75 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7961 (t-90) REVERT: k 75 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7722 (t-90) REVERT: k 189 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8196 (tt) REVERT: k 502 SER cc_start: 0.8330 (m) cc_final: 0.8027 (p) REVERT: l 183 GLN cc_start: 0.7539 (mp10) cc_final: 0.7038 (mp10) outliers start: 98 outliers final: 59 residues processed: 612 average time/residue: 0.3014 time to fit residues: 284.6190 Evaluate side-chains 612 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 543 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 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 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 615 LEU 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 256 VAL 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 143 VAL Chi-restraints excluded: chain f residue 182 THR Chi-restraints excluded: chain f residue 256 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 503 MET Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain g residue 615 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 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 503 MET 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 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 143 VAL Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 499 VAL Chi-restraints excluded: chain l residue 501 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 0.8980 chunk 371 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 419 optimal weight: 5.9990 chunk 228 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 486 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 236 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** i 606 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.181323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142892 restraints weight = 48593.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138981 restraints weight = 90000.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141332 restraints weight = 81586.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141356 restraints weight = 49074.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141831 restraints weight = 48816.652| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41520 Z= 0.148 Angle : 0.565 12.343 56472 Z= 0.285 Chirality : 0.041 0.163 6144 Planarity : 0.004 0.063 7332 Dihedral : 4.125 22.841 5700 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.49 % Allowed : 14.82 % Favored : 82.69 % 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 are not related in a simple way. whole: 1.38 (0.12), residues: 5004 helix: 2.29 (0.10), residues: 2832 sheet: 0.79 (0.24), residues: 480 loop : -1.56 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG j 207 TYR 0.023 0.001 TYR g 608 PHE 0.010 0.001 PHE i 600 TRP 0.013 0.001 TRP j 258 HIS 0.008 0.001 HIS g 31 Details of bonding type rmsd covalent geometry : bond 0.00360 (41520) covalent geometry : angle 0.56455 (56472) hydrogen bonds : bond 0.04221 ( 2167) hydrogen bonds : angle 4.04307 ( 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 662 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 557 time to evaluate : 1.532 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: 0.8210 (OUTLIER) cc_final: 0.7949 (t-90) REVERT: b 75 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7862 (t-90) REVERT: b 593 GLU cc_start: 0.7937 (tp30) cc_final: 0.7719 (tp30) REVERT: c 47 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8113 (pp) REVERT: c 183 GLN cc_start: 0.7649 (mp10) cc_final: 0.7168 (mp10) REVERT: d 83 TYR cc_start: 0.7973 (t80) cc_final: 0.7537 (t80) REVERT: d 207 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7218 (mpp80) REVERT: e 237 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7820 (mtp-110) REVERT: e 592 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7923 (tm-30) REVERT: g 75 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7972 (t-90) REVERT: h 75 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7872 (t-90) REVERT: i 47 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (pp) REVERT: i 160 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8463 (t80) REVERT: j 75 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.8016 (t-90) REVERT: j 192 HIS cc_start: 0.7823 (t-90) cc_final: 0.7418 (t-90) REVERT: k 75 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7743 (t-90) REVERT: k 189 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8247 (tt) REVERT: k 502 SER cc_start: 0.8345 (m) cc_final: 0.8136 (p) outliers start: 105 outliers final: 80 residues processed: 612 average time/residue: 0.2826 time to fit residues: 267.5857 Evaluate side-chains 630 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 540 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 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 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 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 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 584 THR Chi-restraints excluded: chain c residue 615 LEU 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 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 33 THR 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 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 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 499 VAL Chi-restraints excluded: chain g residue 503 MET Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain g residue 615 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 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 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 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 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 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 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 143 VAL Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 501 LYS 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: 0.9980 chunk 367 optimal weight: 0.6980 chunk 337 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 471 optimal weight: 0.9990 chunk 413 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 606 GLN f 236 HIS h 57 ASN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.180891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143916 restraints weight = 48325.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140075 restraints weight = 95043.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142087 restraints weight = 87112.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141975 restraints weight = 52139.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.145018 restraints weight = 47628.554| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 41520 Z= 0.154 Angle : 0.574 12.469 56472 Z= 0.290 Chirality : 0.041 0.162 6144 Planarity : 0.004 0.046 7332 Dihedral : 4.138 22.139 5700 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.77 % Allowed : 15.01 % Favored : 82.22 % 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 are not related in a simple way. whole: 1.36 (0.12), residues: 5004 helix: 2.29 (0.10), residues: 2832 sheet: 0.75 (0.24), residues: 480 loop : -1.59 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG j 207 TYR 0.019 0.001 TYR g 608 PHE 0.013 0.001 PHE i 600 TRP 0.012 0.001 TRP l 532 HIS 0.008 0.001 HIS d 31 Details of bonding type rmsd covalent geometry : bond 0.00377 (41520) covalent geometry : angle 0.57354 (56472) hydrogen bonds : bond 0.04262 ( 2167) hydrogen bonds : angle 4.04272 ( 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 663 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 546 time to evaluate : 1.610 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: 0.8159 (OUTLIER) cc_final: 0.7864 (t-90) REVERT: a 307 ARG cc_start: 0.6570 (mtt-85) cc_final: 0.6262 (mtt-85) REVERT: b 75 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7867 (t-90) REVERT: c 47 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8115 (pp) REVERT: c 183 GLN cc_start: 0.7642 (mp10) cc_final: 0.7270 (mp10) REVERT: e 237 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7667 (mtp-110) REVERT: g 75 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7990 (t-90) REVERT: h 75 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7782 (t-90) REVERT: i 47 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8284 (pp) REVERT: i 160 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8472 (t80) REVERT: i 183 GLN cc_start: 0.7781 (mp10) cc_final: 0.7233 (mp10) REVERT: j 192 HIS cc_start: 0.7752 (t-90) cc_final: 0.7469 (t-90) REVERT: k 75 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7677 (t-90) REVERT: k 189 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8309 (tt) outliers start: 117 outliers final: 93 residues processed: 614 average time/residue: 0.2944 time to fit residues: 280.0982 Evaluate side-chains 641 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 539 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 292 VAL 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 230 VAL 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 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 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 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 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 496 ILE Chi-restraints excluded: chain e residue 615 LEU 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 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 503 MET Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain g residue 615 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 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 503 MET 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 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 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 189 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 136 LEU Chi-restraints excluded: chain l residue 143 VAL Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 292 VAL Chi-restraints excluded: chain l residue 501 LYS Chi-restraints excluded: chain l residue 584 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 146 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 417 optimal weight: 1.9990 chunk 483 optimal weight: 0.1980 chunk 353 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 622 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.187579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154914 restraints weight = 47385.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.152023 restraints weight = 93856.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.153407 restraints weight = 89992.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.153153 restraints weight = 56711.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.154299 restraints weight = 50191.036| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 41520 Z= 0.107 Angle : 0.540 12.332 56472 Z= 0.270 Chirality : 0.040 0.169 6144 Planarity : 0.004 0.047 7332 Dihedral : 3.944 22.134 5700 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.68 % Allowed : 16.22 % Favored : 82.10 % 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 are not related in a simple way. whole: 1.52 (0.12), residues: 5004 helix: 2.42 (0.10), residues: 2832 sheet: 0.91 (0.24), residues: 480 loop : -1.54 (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 g 608 PHE 0.010 0.001 PHE i 600 TRP 0.011 0.001 TRP l 532 HIS 0.007 0.001 HIS f 236 Details of bonding type rmsd covalent geometry : bond 0.00238 (41520) covalent geometry : angle 0.53983 (56472) hydrogen bonds : bond 0.03447 ( 2167) hydrogen bonds : angle 3.88853 ( 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 652 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 581 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: a 75 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7977 (t-90) REVERT: a 307 ARG cc_start: 0.6491 (mtt-85) cc_final: 0.6245 (mtt-85) REVERT: b 75 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7879 (t-90) REVERT: b 207 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7205 (mtt90) REVERT: c 47 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (pp) REVERT: c 183 GLN cc_start: 0.7630 (mt0) cc_final: 0.7216 (mp10) REVERT: d 47 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8227 (pp) REVERT: d 83 TYR cc_start: 0.7841 (t80) cc_final: 0.7362 (t80) REVERT: d 183 GLN cc_start: 0.7700 (mp10) cc_final: 0.7107 (mp10) REVERT: d 207 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7479 (mpp80) REVERT: e 237 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7638 (mtp-110) REVERT: g 47 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8107 (pp) REVERT: g 75 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7932 (t-90) REVERT: h 75 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7834 (t-90) REVERT: i 47 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8169 (pp) REVERT: i 160 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8402 (t80) REVERT: i 183 GLN cc_start: 0.7749 (mp10) cc_final: 0.7057 (mp10) REVERT: i 496 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8189 (mt) REVERT: j 47 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8155 (pp) REVERT: j 192 HIS cc_start: 0.7698 (t-90) cc_final: 0.7324 (t-90) REVERT: k 75 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7665 (t-90) REVERT: l 183 GLN cc_start: 0.7975 (mp10) cc_final: 0.7287 (mp10) outliers start: 71 outliers final: 46 residues processed: 621 average time/residue: 0.2957 time to fit residues: 284.9679 Evaluate side-chains 612 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 554 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 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 256 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 615 LEU Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 142 LEU 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 292 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 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 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 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 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 47 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain k residue 36 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 182 THR Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 501 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 364 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 466 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 413 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 132 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 606 GLN ** f 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 297 ASN i 235 ASN ** l 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.186685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.155048 restraints weight = 47587.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.153279 restraints weight = 92826.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.154129 restraints weight = 87156.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153680 restraints weight = 57452.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.152558 restraints weight = 52569.210| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41520 Z= 0.123 Angle : 0.554 12.597 56472 Z= 0.277 Chirality : 0.040 0.168 6144 Planarity : 0.004 0.054 7332 Dihedral : 3.924 20.858 5700 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.82 % Allowed : 16.48 % Favored : 81.70 % 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 are not related in a simple way. whole: 1.51 (0.12), residues: 5004 helix: 2.41 (0.10), residues: 2832 sheet: 0.89 (0.24), residues: 480 loop : -1.55 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG h 207 TYR 0.026 0.001 TYR d 608 PHE 0.024 0.001 PHE c 600 TRP 0.011 0.001 TRP l 532 HIS 0.006 0.001 HIS d 31 Details of bonding type rmsd covalent geometry : bond 0.00291 (41520) covalent geometry : angle 0.55444 (56472) hydrogen bonds : bond 0.03727 ( 2167) hydrogen bonds : angle 3.87948 ( 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 642 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 565 time to evaluate : 1.613 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 307 ARG cc_start: 0.6535 (mtt-85) cc_final: 0.6263 (mtt-85) REVERT: b 75 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7915 (t-90) REVERT: b 207 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7235 (mtt90) REVERT: c 47 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7951 (pp) REVERT: c 183 GLN cc_start: 0.7668 (mt0) cc_final: 0.7265 (mp10) REVERT: d 47 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8201 (pp) REVERT: d 75 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7750 (t-90) REVERT: e 237 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7640 (mtp-110) REVERT: g 75 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7972 (t-90) REVERT: h 75 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7870 (t-90) REVERT: i 47 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8232 (pp) REVERT: i 183 GLN cc_start: 0.7787 (mp10) cc_final: 0.7080 (mp10) REVERT: j 47 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8250 (pp) REVERT: j 192 HIS cc_start: 0.7779 (t-90) cc_final: 0.7401 (t-90) REVERT: j 237 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7624 (mtp-110) REVERT: k 75 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7751 (t-90) REVERT: k 189 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8346 (tt) REVERT: l 183 GLN cc_start: 0.7785 (mp10) cc_final: 0.7085 (mp10) outliers start: 77 outliers final: 58 residues processed: 610 average time/residue: 0.3005 time to fit residues: 283.2229 Evaluate side-chains 623 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 555 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 143 VAL 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 256 VAL Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 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 615 LEU Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 75 HIS 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 292 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 230 VAL 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 292 VAL 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 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 178 GLU Chi-restraints excluded: chain i residue 185 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 143 VAL Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 496 ILE Chi-restraints excluded: chain j residue 503 MET 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 292 VAL Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 501 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 356 optimal weight: 2.9990 chunk 322 optimal weight: 0.0170 chunk 9 optimal weight: 0.0770 chunk 230 optimal weight: 0.2980 chunk 120 optimal weight: 4.9990 chunk 444 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 326 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 622 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 = 0.4043 r_free = 0.4043 target = 0.188828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.157125 restraints weight = 47299.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.155300 restraints weight = 87767.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156149 restraints weight = 89960.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155874 restraints weight = 56028.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157046 restraints weight = 49532.651| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 41520 Z= 0.105 Angle : 0.543 12.336 56472 Z= 0.271 Chirality : 0.039 0.168 6144 Planarity : 0.004 0.055 7332 Dihedral : 3.808 20.437 5700 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.52 % Allowed : 17.07 % Favored : 81.42 % 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 are not related in a simple way. whole: 1.65 (0.12), residues: 5004 helix: 2.49 (0.10), residues: 2832 sheet: 1.30 (0.25), residues: 456 loop : -1.48 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG g 84 TYR 0.030 0.001 TYR d 608 PHE 0.022 0.001 PHE c 600 TRP 0.011 0.001 TRP l 532 HIS 0.005 0.001 HIS k 622 Details of bonding type rmsd covalent geometry : bond 0.00231 (41520) covalent geometry : angle 0.54304 (56472) hydrogen bonds : bond 0.03251 ( 2167) hydrogen bonds : angle 3.78715 ( 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 639 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 575 time to evaluate : 1.368 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 307 ARG cc_start: 0.6444 (mtt-85) cc_final: 0.6188 (mtt-85) REVERT: b 75 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7834 (t-90) REVERT: b 207 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7070 (mtt90) REVERT: c 47 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (pp) REVERT: c 183 GLN cc_start: 0.7347 (mt0) cc_final: 0.6905 (mp10) REVERT: d 75 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7666 (t-90) REVERT: d 207 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7317 (mpp80) REVERT: e 237 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7545 (mtp-110) REVERT: g 47 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8085 (pp) REVERT: i 47 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8115 (pp) REVERT: k 75 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7661 (t-90) REVERT: k 189 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7898 (tt) REVERT: l 183 GLN cc_start: 0.7422 (mp10) cc_final: 0.6981 (mp10) outliers start: 64 outliers final: 42 residues processed: 609 average time/residue: 0.2875 time to fit residues: 270.9771 Evaluate side-chains 600 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 551 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 143 VAL 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 256 VAL Chi-restraints excluded: chain b residue 499 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 185 LEU 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 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 292 VAL Chi-restraints excluded: chain e residue 496 ILE 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 143 VAL Chi-restraints excluded: chain g residue 253 GLU Chi-restraints excluded: chain g residue 543 LEU Chi-restraints excluded: chain h residue 143 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 185 LEU Chi-restraints excluded: chain i residue 256 VAL 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 503 MET 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 143 VAL Chi-restraints excluded: chain k residue 189 LEU Chi-restraints excluded: chain k residue 292 VAL Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 501 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 304 optimal weight: 3.9990 chunk 394 optimal weight: 0.8980 chunk 49 optimal weight: 0.0770 chunk 471 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 392 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 50 optimal weight: 0.0770 chunk 431 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 297 ASN d 606 GLN e 297 ASN f 236 HIS f 622 HIS j 297 ASN ** 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 = 0.4177 r_free = 0.4177 target = 0.194059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155438 restraints weight = 49161.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155836 restraints weight = 67692.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155976 restraints weight = 58184.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156825 restraints weight = 30776.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159615 restraints weight = 25543.896| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41520 Z= 0.119 Angle : 0.556 12.486 56472 Z= 0.276 Chirality : 0.040 0.163 6144 Planarity : 0.004 0.056 7332 Dihedral : 3.829 19.809 5700 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.59 % Allowed : 17.14 % Favored : 81.27 % 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 are not related in a simple way. whole: 1.57 (0.12), residues: 5004 helix: 2.44 (0.10), residues: 2844 sheet: 0.95 (0.24), residues: 480 loop : -1.52 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG g 307 TYR 0.028 0.001 TYR d 608 PHE 0.022 0.001 PHE c 600 TRP 0.010 0.001 TRP l 532 HIS 0.006 0.001 HIS g 31 Details of bonding type rmsd covalent geometry : bond 0.00279 (41520) covalent geometry : angle 0.55613 (56472) hydrogen bonds : bond 0.03542 ( 2167) hydrogen bonds : angle 3.81064 ( 6393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6926.00 seconds wall clock time: 120 minutes 19.24 seconds (7219.24 seconds total)