Starting phenix.real_space_refine on Thu Mar 5 15:21:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jz2_22528/03_2026/7jz2_22528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jz2_22528/03_2026/7jz2_22528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jz2_22528/03_2026/7jz2_22528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jz2_22528/03_2026/7jz2_22528_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jz2_22528/03_2026/7jz2_22528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jz2_22528/03_2026/7jz2_22528.map" } resolution = 2.5 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.172 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: 7 Type Number sf(0) Gaussians Fe 30 7.16 5 P 9 5.49 5 S 186 5.16 5 Na 3 4.78 5 C 14520 2.51 5 N 3921 2.21 5 O 4197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22866 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "C" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "E" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "G" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "I" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "J" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "K" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'HEM': 1, 'UQ2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4298 SG CYS B 75 79.724 104.845 57.102 1.00 25.54 S ATOM 4931 SG CYS B 155 76.201 91.973 66.627 1.00 22.51 S ATOM 5407 SG CYS B 216 71.860 97.703 66.077 1.00 23.12 S ATOM 4892 SG CYS B 149 73.317 91.509 61.104 1.00 26.11 S ATOM 4914 SG CYS B 152 78.004 96.628 62.112 1.00 22.99 S ATOM 4956 SG CYS B 159 78.230 89.297 74.675 1.00 23.87 S ATOM 11744 SG CYS F 75 29.864 51.387 57.064 1.00 25.46 S ATOM 12377 SG CYS F 155 42.751 54.826 66.599 1.00 22.34 S ATOM 12853 SG CYS F 216 39.979 48.193 66.058 1.00 22.71 S ATOM 12338 SG CYS F 149 44.608 52.556 61.083 1.00 26.26 S ATOM 12360 SG CYS F 152 37.826 54.038 62.080 1.00 22.64 S ATOM 12402 SG CYS F 159 44.035 57.939 74.644 1.00 23.27 S ATOM 19190 SG CYS J 75 101.028 34.907 57.031 1.00 24.60 S ATOM 19823 SG CYS J 155 91.669 44.358 66.618 1.00 22.22 S ATOM 20299 SG CYS J 216 98.798 45.264 66.040 1.00 23.30 S ATOM 19784 SG CYS J 149 92.682 47.102 61.098 1.00 25.85 S ATOM 19806 SG CYS J 152 94.785 40.484 62.081 1.00 23.16 S ATOM 19848 SG CYS J 159 88.372 43.915 74.680 1.00 23.87 S Time building chain proxies: 5.62, per 1000 atoms: 0.25 Number of scatterers: 22866 At special positions: 0 Unit cell: (131.76, 135, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 30 26.01 S 186 16.00 P 9 15.00 Na 3 11.00 O 4197 8.00 N 3921 7.00 C 14520 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 159 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 206 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 212 " pdb=" F3S F 303 " pdb="FE1 F3S F 303 " - pdb=" SG CYS F 159 " pdb="FE3 F3S F 303 " - pdb=" SG CYS F 206 " pdb="FE4 F3S F 303 " - pdb=" SG CYS F 212 " pdb=" F3S J 303 " pdb="FE1 F3S J 303 " - pdb=" SG CYS J 159 " pdb="FE3 F3S J 303 " - pdb=" SG CYS J 206 " pdb="FE4 F3S J 303 " - pdb=" SG CYS J 212 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 75 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 55 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 60 " pdb=" FES F 301 " pdb="FE1 FES F 301 " - pdb=" SG CYS F 75 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 55 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 60 " pdb=" FES J 301 " pdb="FE1 FES J 301 " - pdb=" SG CYS J 75 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 55 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 60 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 216 " pdb=" SF4 F 302 " pdb="FE4 SF4 F 302 " - pdb=" SG CYS F 152 " pdb="FE1 SF4 F 302 " - pdb=" SG CYS F 155 " pdb="FE3 SF4 F 302 " - pdb=" SG CYS F 149 " pdb="FE2 SF4 F 302 " - pdb=" SG CYS F 216 " pdb=" SF4 J 302 " pdb="FE4 SF4 J 302 " - pdb=" SG CYS J 152 " pdb="FE1 SF4 J 302 " - pdb=" SG CYS J 155 " pdb="FE3 SF4 J 302 " - pdb=" SG CYS J 149 " pdb="FE2 SF4 J 302 " - pdb=" SG CYS J 216 " Number of angles added : 75 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 52.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 64 through 76 removed outlier: 4.275A pdb=" N HIS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 103 Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 140 through 157 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.859A pdb=" N LEU A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 433 through 450 removed outlier: 3.969A pdb=" N VAL A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 507 through 533 removed outlier: 3.680A pdb=" N VAL A 511 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.892A pdb=" N LEU B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.787A pdb=" N ILE B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.685A pdb=" N ARG B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.522A pdb=" N ALA B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 54 removed outlier: 3.954A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 102 through 129 removed outlier: 3.503A pdb=" N LEU C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 54 through 84 Processing helix chain 'D' and resid 86 through 113 Processing helix chain 'E' and resid 16 through 29 Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.275A pdb=" N HIS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 140 through 157 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 220 through 230 Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.858A pdb=" N LEU E 406 " --> pdb=" O GLY E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 427 Processing helix chain 'E' and resid 433 through 450 removed outlier: 3.969A pdb=" N VAL E 437 " --> pdb=" O SER E 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU E 438 " --> pdb=" O GLU E 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU E 444 " --> pdb=" O SER E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 471 Processing helix chain 'E' and resid 476 through 495 Processing helix chain 'E' and resid 507 through 533 removed outlier: 3.680A pdb=" N VAL E 511 " --> pdb=" O ASN E 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.891A pdb=" N LEU F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 117 removed outlier: 3.786A pdb=" N ILE F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 142 Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 189 through 197 removed outlier: 3.684A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 221 through 238 removed outlier: 3.521A pdb=" N ALA F 225 " --> pdb=" O ASN F 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 54 removed outlier: 3.954A pdb=" N GLY G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 66 Processing helix chain 'G' and resid 67 through 97 Processing helix chain 'G' and resid 102 through 129 removed outlier: 3.503A pdb=" N LEU G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 40 Processing helix chain 'H' and resid 44 through 52 Processing helix chain 'H' and resid 54 through 84 Processing helix chain 'H' and resid 86 through 113 Processing helix chain 'I' and resid 16 through 29 Processing helix chain 'I' and resid 44 through 49 Processing helix chain 'I' and resid 64 through 76 removed outlier: 4.276A pdb=" N HIS I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 103 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 140 through 157 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 220 through 230 Processing helix chain 'I' and resid 402 through 418 removed outlier: 3.859A pdb=" N LEU I 406 " --> pdb=" O GLY I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 427 Processing helix chain 'I' and resid 433 through 450 removed outlier: 3.970A pdb=" N VAL I 437 " --> pdb=" O SER I 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU I 438 " --> pdb=" O GLU I 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG I 443 " --> pdb=" O ALA I 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU I 444 " --> pdb=" O SER I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 471 Processing helix chain 'I' and resid 476 through 495 Processing helix chain 'I' and resid 507 through 533 removed outlier: 3.679A pdb=" N VAL I 511 " --> pdb=" O ASN I 507 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 44 Processing helix chain 'J' and resid 75 through 77 No H-bonds generated for 'chain 'J' and resid 75 through 77' Processing helix chain 'J' and resid 78 through 83 removed outlier: 3.892A pdb=" N LEU J 82 " --> pdb=" O PRO J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 removed outlier: 3.787A pdb=" N ILE J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 142 Processing helix chain 'J' and resid 155 through 158 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'J' and resid 171 through 184 Processing helix chain 'J' and resid 189 through 197 removed outlier: 3.685A pdb=" N ARG J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 216 Processing helix chain 'J' and resid 221 through 238 removed outlier: 3.521A pdb=" N ALA J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 54 removed outlier: 3.955A pdb=" N GLY K 42 " --> pdb=" O PHE K 38 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 66 Processing helix chain 'K' and resid 67 through 97 Processing helix chain 'K' and resid 102 through 129 removed outlier: 3.504A pdb=" N LEU K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 Processing helix chain 'L' and resid 44 through 52 Processing helix chain 'L' and resid 54 through 84 Processing helix chain 'L' and resid 86 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.299A pdb=" N ARG A 6 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 177 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS A 171 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 179 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU A 169 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 181 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.910A pdb=" N THR A 159 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA A 10 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU A 36 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA A 368 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL A 233 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.623A pdb=" N GLN A 240 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 361 removed outlier: 5.520A pdb=" N ILE A 360 " --> pdb=" O CYS A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 25 Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7 removed outlier: 6.299A pdb=" N ARG E 6 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL E 177 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS E 171 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY E 179 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU E 169 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR E 181 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.911A pdb=" N THR E 159 " --> pdb=" O CYS E 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA E 10 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU E 36 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 12 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA E 368 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'E' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL E 233 " --> pdb=" O TYR E 559 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 239 through 242 removed outlier: 6.622A pdb=" N GLN E 240 " --> pdb=" O HIS E 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 360 through 361 removed outlier: 5.521A pdb=" N ILE E 360 " --> pdb=" O CYS E 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 536 through 537 Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 25 Processing sheet with id=AB8, first strand: chain 'I' and resid 5 through 7 removed outlier: 6.298A pdb=" N ARG I 6 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL I 177 " --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS I 171 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY I 179 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU I 169 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR I 181 " --> pdb=" O LEU I 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 159 through 161 removed outlier: 3.911A pdb=" N THR I 159 " --> pdb=" O CYS I 33 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA I 10 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I 36 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL I 12 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA I 368 " --> pdb=" O VAL I 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'I' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL I 233 " --> pdb=" O TYR I 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 239 through 242 removed outlier: 6.622A pdb=" N GLN I 240 " --> pdb=" O HIS I 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 360 through 361 removed outlier: 5.520A pdb=" N ILE I 360 " --> pdb=" O CYS I 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 536 through 537 Processing sheet with id=AC6, first strand: chain 'J' and resid 19 through 25 1221 hydrogen bonds defined for protein. 3519 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: 3.69 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.74: 23046 1.74 - 2.29: 321 2.29 - 2.84: 9 2.84 - 3.40: 0 3.40 - 3.95: 9 Bond restraints: 23385 Sorted by residual: bond pdb=" S4 F3S J 303 " pdb="FE1 F3S J 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S F 303 " pdb="FE1 F3S F 303 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.951 -1.651 2.00e-02 2.50e+03 6.81e+03 bond pdb=" S2 F3S F 303 " pdb="FE3 F3S F 303 " ideal model delta sigma weight residual 2.300 3.950 -1.650 2.00e-02 2.50e+03 6.81e+03 ... (remaining 23380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.99: 31725 9.99 - 19.97: 15 19.97 - 29.96: 3 29.96 - 39.95: 21 39.95 - 49.93: 6 Bond angle restraints: 31770 Sorted by residual: angle pdb=" S1 F3S J 303 " pdb="FE4 F3S J 303 " pdb=" S3 F3S J 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S F 303 " pdb="FE4 F3S F 303 " pdb=" S3 F3S F 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 64.83 49.92 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S3 F3S J 303 " pdb="FE1 F3S J 303 " pdb=" S4 F3S J 303 " ideal model delta sigma weight residual 112.59 64.30 48.29 3.00e+00 1.11e-01 2.59e+02 angle pdb=" S3 F3S F 303 " pdb="FE1 F3S F 303 " pdb=" S4 F3S F 303 " ideal model delta sigma weight residual 112.59 64.31 48.28 3.00e+00 1.11e-01 2.59e+02 ... (remaining 31765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 12488 16.63 - 33.25: 972 33.25 - 49.88: 292 49.88 - 66.50: 90 66.50 - 83.13: 36 Dihedral angle restraints: 13878 sinusoidal: 5664 harmonic: 8214 Sorted by residual: dihedral pdb=" C2D HEM K 201 " pdb=" C3D HEM K 201 " pdb=" CAD HEM K 201 " pdb=" CBD HEM K 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.81 -67.81 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM D 201 " pdb=" C3D HEM D 201 " pdb=" CAD HEM D 201 " pdb=" CBD HEM D 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.71 -67.71 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM G 201 " pdb=" C3D HEM G 201 " pdb=" CAD HEM G 201 " pdb=" CBD HEM G 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.70 -67.70 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 13875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.605: 3504 3.605 - 7.210: 0 7.210 - 10.816: 0 10.816 - 14.421: 0 14.421 - 18.026: 3 Chirality restraints: 3507 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.26 18.03 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S F 303 " pdb="FE1 F3S F 303 " pdb="FE3 F3S F 303 " pdb="FE4 F3S F 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S J 303 " pdb="FE1 F3S J 303 " pdb="FE3 F3S J 303 " pdb="FE4 F3S J 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 ... (remaining 3504 not shown) Planarity restraints: 4029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 113 " 0.007 2.00e-02 2.50e+03 5.32e-03 7.07e-01 pdb=" CG TRP L 113 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP L 113 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 113 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 113 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 109 " 0.004 2.00e-02 2.50e+03 8.38e-03 7.02e-01 pdb=" C PHE D 109 " -0.014 2.00e-02 2.50e+03 pdb=" O PHE D 109 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL D 110 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 109 " -0.004 2.00e-02 2.50e+03 8.36e-03 6.98e-01 pdb=" C PHE L 109 " 0.014 2.00e-02 2.50e+03 pdb=" O PHE L 109 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL L 110 " -0.005 2.00e-02 2.50e+03 ... (remaining 4026 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 395 2.64 - 3.20: 22686 3.20 - 3.77: 36860 3.77 - 4.33: 52080 4.33 - 4.90: 85072 Nonbonded interactions: 197093 Sorted by model distance: nonbonded pdb=" OD1 ASP J 46 " pdb=" OG SER J 48 " model vdw 2.070 3.040 nonbonded pdb=" OD1 ASP F 46 " pdb=" OG SER F 48 " model vdw 2.070 3.040 nonbonded pdb=" OD1 ASP B 46 " pdb=" OG SER B 48 " model vdw 2.070 3.040 nonbonded pdb=" NH1 ARG J 205 " pdb=" OD1 ASP L 82 " model vdw 2.114 3.120 nonbonded pdb=" OE1 GLU E 94 " pdb=" NH1 ARG E 413 " model vdw 2.115 3.120 ... (remaining 197088 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = (chain 'C' and resid 5 through 129) selection = (chain 'G' and resid 5 through 129) selection = (chain 'K' and resid 5 through 129) } ncs_group { reference = (chain 'D' and resid 3 through 115) selection = (chain 'H' and resid 3 through 115) selection = (chain 'L' and resid 3 through 115) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.360 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 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:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.042 1.702 23420 Z= 1.972 Angle : 1.922 70.119 31845 Z= 0.548 Chirality : 0.528 18.026 3507 Planarity : 0.002 0.019 4029 Dihedral : 14.261 83.128 8604 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 35.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.38 % Allowed : 2.39 % Favored : 96.23 % 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: -2.16 (0.14), residues: 2841 helix: 0.25 (0.13), residues: 1404 sheet: -3.15 (0.28), residues: 165 loop : -3.27 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 413 TYR 0.011 0.001 TYR B 8 PHE 0.010 0.001 PHE E 411 TRP 0.015 0.001 TRP L 113 HIS 0.003 0.000 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.03272 (23385) covalent geometry : angle 1.28065 (31770) hydrogen bonds : bond 0.12098 ( 1221) hydrogen bonds : angle 5.65316 ( 3519) metal coordination : bond 0.71833 ( 30) metal coordination : angle 29.55529 ( 75) Misc. bond : bond 0.38835 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 598 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6830 (mtp) cc_final: 0.6593 (mtp) REVERT: A 227 ILE cc_start: 0.7298 (mt) cc_final: 0.6841 (mt) REVERT: A 236 MET cc_start: 0.7449 (mmp) cc_final: 0.6907 (mmp) REVERT: A 443 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 1 MET cc_start: 0.5214 (ptt) cc_final: 0.4115 (mpp) REVERT: B 41 GLN cc_start: 0.6981 (tt0) cc_final: 0.6644 (mt0) REVERT: D 77 TRP cc_start: 0.7643 (t60) cc_final: 0.7348 (t-100) REVERT: E 209 TYR cc_start: 0.7159 (m-80) cc_final: 0.6879 (m-80) REVERT: E 227 ILE cc_start: 0.7479 (mt) cc_final: 0.7077 (mt) REVERT: E 568 ARG cc_start: 0.7382 (mtt180) cc_final: 0.7083 (mtt180) REVERT: F 9 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: F 232 MET cc_start: 0.7783 (mtp) cc_final: 0.7388 (mtp) REVERT: G 93 MET cc_start: 0.6906 (mtp) cc_final: 0.6495 (mtp) REVERT: H 56 PHE cc_start: 0.7072 (t80) cc_final: 0.5613 (m-80) REVERT: I 227 ILE cc_start: 0.7064 (mt) cc_final: 0.6598 (mt) REVERT: I 420 GLN cc_start: 0.6644 (tp40) cc_final: 0.6319 (tp40) REVERT: I 446 ARG cc_start: 0.7473 (tmm160) cc_final: 0.7234 (tmm160) REVERT: I 471 PHE cc_start: 0.6564 (m-80) cc_final: 0.6330 (m-80) REVERT: I 568 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7118 (mtt-85) REVERT: J 67 MET cc_start: 0.6782 (mtm) cc_final: 0.6422 (mtm) REVERT: J 235 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6774 (mm110) REVERT: L 45 TYR cc_start: 0.7261 (t80) cc_final: 0.7059 (t80) REVERT: L 56 PHE cc_start: 0.7054 (t80) cc_final: 0.5779 (m-80) outliers start: 33 outliers final: 7 residues processed: 626 average time/residue: 0.6141 time to fit residues: 439.4457 Evaluate side-chains 492 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 485 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 352 THR Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 173 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 450 ASN A 452 ASN A 531 ASN B 71 ASN B 123 ASN B 133 HIS B 207 HIS B 211 ASN B 237 ASN C 91 HIS D 14 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS E 173 GLN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN E 452 ASN E 496 ASN E 518 ASN E 531 ASN F 71 ASN F 207 HIS F 211 ASN F 228 HIS F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS H 14 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 143 HIS ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 450 ASN I 452 ASN I 518 ASN I 531 ASN J 71 ASN J 123 ASN J 133 HIS J 207 HIS J 228 HIS J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS L 14 HIS L 94 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.160805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143894 restraints weight = 30052.582| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.07 r_work: 0.3668 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 23420 Z= 0.266 Angle : 1.578 65.598 31845 Z= 0.492 Chirality : 0.063 1.586 3507 Planarity : 0.005 0.044 4029 Dihedral : 9.197 76.836 3437 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.27 % Allowed : 12.56 % Favored : 83.17 % 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: -0.86 (0.15), residues: 2841 helix: 1.21 (0.13), residues: 1437 sheet: -2.76 (0.28), residues: 189 loop : -2.51 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 578 TYR 0.022 0.002 TYR B 8 PHE 0.023 0.002 PHE D 60 TRP 0.018 0.002 TRP H 113 HIS 0.006 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00580 (23385) covalent geometry : angle 1.25274 (31770) hydrogen bonds : bond 0.05287 ( 1221) hydrogen bonds : angle 4.75949 ( 3519) metal coordination : bond 0.02655 ( 30) metal coordination : angle 19.81821 ( 75) Misc. bond : bond 0.18321 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 538 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7324 (m-30) cc_final: 0.6799 (m-30) REVERT: A 31 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6864 (mp10) REVERT: A 46 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8408 (m) REVERT: A 236 MET cc_start: 0.7708 (mmp) cc_final: 0.7505 (mmp) REVERT: A 438 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: A 471 PHE cc_start: 0.7053 (m-80) cc_final: 0.6518 (m-80) REVERT: A 476 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6594 (mt-10) REVERT: A 488 LYS cc_start: 0.5737 (OUTLIER) cc_final: 0.5507 (mmmm) REVERT: A 490 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6855 (mp) REVERT: A 568 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7110 (mtt180) REVERT: B 1 MET cc_start: 0.5877 (ptt) cc_final: 0.4546 (mpp) REVERT: B 2 ARG cc_start: 0.6891 (ptm160) cc_final: 0.6196 (ptm160) REVERT: B 9 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7413 (mmm-85) REVERT: B 33 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6770 (ptt) REVERT: B 144 ASP cc_start: 0.8001 (m-30) cc_final: 0.7572 (m-30) REVERT: C 101 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: D 27 THR cc_start: 0.6852 (p) cc_final: 0.6299 (m) REVERT: D 77 TRP cc_start: 0.7926 (t60) cc_final: 0.7222 (t-100) REVERT: E 31 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6070 (mp10) REVERT: E 46 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8188 (m) REVERT: E 196 ARG cc_start: 0.7238 (mtp180) cc_final: 0.7016 (mtp180) REVERT: E 227 ILE cc_start: 0.7532 (mt) cc_final: 0.7247 (mt) REVERT: E 352 THR cc_start: 0.7992 (t) cc_final: 0.7547 (m) REVERT: E 438 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: E 449 ASN cc_start: 0.6472 (m-40) cc_final: 0.6084 (m-40) REVERT: E 455 ASP cc_start: 0.7496 (t0) cc_final: 0.7271 (t0) REVERT: E 568 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7449 (mtt180) REVERT: E 578 ARG cc_start: 0.6835 (ttt90) cc_final: 0.6582 (tpt-90) REVERT: E 581 PHE cc_start: 0.8343 (m-80) cc_final: 0.7903 (m-80) REVERT: F 2 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6566 (ttt90) REVERT: F 33 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6640 (ptt) REVERT: F 102 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7700 (t70) REVERT: F 235 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7057 (mm110) REVERT: G 81 LEU cc_start: 0.7352 (tp) cc_final: 0.7124 (tt) REVERT: G 93 MET cc_start: 0.7385 (mtp) cc_final: 0.6978 (mtp) REVERT: G 123 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7333 (mp) REVERT: H 56 PHE cc_start: 0.7465 (t80) cc_final: 0.5080 (m-80) REVERT: I 31 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6917 (mm110) REVERT: I 46 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8426 (m) REVERT: I 187 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7300 (p) REVERT: I 227 ILE cc_start: 0.7409 (mt) cc_final: 0.7144 (mt) REVERT: I 420 GLN cc_start: 0.7027 (tp40) cc_final: 0.6637 (tp40) REVERT: I 450 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.6476 (t0) REVERT: I 455 ASP cc_start: 0.7734 (t0) cc_final: 0.7450 (t0) REVERT: I 520 MET cc_start: 0.8459 (tpt) cc_final: 0.8027 (tpt) REVERT: I 572 ASN cc_start: 0.7129 (t0) cc_final: 0.6733 (t0) REVERT: J 2 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6360 (ptm-80) REVERT: J 67 MET cc_start: 0.7072 (mtm) cc_final: 0.6750 (mtm) REVERT: J 102 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7346 (t70) REVERT: J 109 GLN cc_start: 0.8138 (mt0) cc_final: 0.7921 (mt0) REVERT: J 235 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6712 (mm110) REVERT: K 101 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: L 56 PHE cc_start: 0.7512 (t80) cc_final: 0.5381 (m-80) REVERT: L 77 TRP cc_start: 0.7911 (t60) cc_final: 0.7142 (t-100) outliers start: 102 outliers final: 34 residues processed: 583 average time/residue: 0.5818 time to fit residues: 390.2296 Evaluate side-chains 553 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 500 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 242 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 220 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 518 ASN B 71 ASN B 237 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 GLN E 452 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 173 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN I 452 ASN J 71 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.162095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145167 restraints weight = 30440.936| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.09 r_work: 0.3681 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 23420 Z= 0.164 Angle : 1.443 84.184 31845 Z= 0.434 Chirality : 0.059 1.457 3507 Planarity : 0.005 0.048 4029 Dihedral : 8.196 77.501 3433 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.52 % Allowed : 15.95 % Favored : 80.53 % 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: -0.23 (0.16), residues: 2841 helix: 1.66 (0.14), residues: 1434 sheet: -2.26 (0.31), residues: 189 loop : -2.13 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 56 TYR 0.027 0.002 TYR H 45 PHE 0.016 0.001 PHE D 60 TRP 0.022 0.001 TRP H 113 HIS 0.005 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00354 (23385) covalent geometry : angle 1.09721 (31770) hydrogen bonds : bond 0.04717 ( 1221) hydrogen bonds : angle 4.54568 ( 3519) metal coordination : bond 0.00823 ( 30) metal coordination : angle 19.35326 ( 75) Misc. bond : bond 0.13776 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 524 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7500 (mm-40) cc_final: 0.6907 (mp10) REVERT: A 46 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8403 (m) REVERT: A 168 ASP cc_start: 0.7725 (m-30) cc_final: 0.7465 (t0) REVERT: A 374 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8296 (ttmp) REVERT: A 438 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: A 471 PHE cc_start: 0.7044 (m-80) cc_final: 0.6501 (m-80) REVERT: A 476 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6516 (mt-10) REVERT: A 490 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6672 (mp) REVERT: B 2 ARG cc_start: 0.6909 (ptm160) cc_final: 0.6391 (ttt90) REVERT: B 33 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6719 (ptt) REVERT: B 56 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7887 (ttp-170) REVERT: B 144 ASP cc_start: 0.7917 (m-30) cc_final: 0.7476 (m-30) REVERT: C 71 LYS cc_start: 0.6434 (mmtm) cc_final: 0.6227 (mmtm) REVERT: C 123 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7171 (mp) REVERT: D 6 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7739 (t) REVERT: D 27 THR cc_start: 0.6792 (p) cc_final: 0.6302 (m) REVERT: E 46 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8184 (m) REVERT: E 196 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7079 (mtp180) REVERT: E 210 GLN cc_start: 0.6791 (tt0) cc_final: 0.6295 (mt0) REVERT: E 227 ILE cc_start: 0.7507 (mt) cc_final: 0.7250 (mt) REVERT: E 243 PRO cc_start: 0.6184 (Cg_endo) cc_final: 0.5945 (Cg_exo) REVERT: E 352 THR cc_start: 0.7929 (t) cc_final: 0.7468 (m) REVERT: E 405 LEU cc_start: 0.6934 (mm) cc_final: 0.6561 (mt) REVERT: E 438 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7005 (tp30) REVERT: E 455 ASP cc_start: 0.7493 (t0) cc_final: 0.7216 (t0) REVERT: E 545 PHE cc_start: 0.6026 (m-80) cc_final: 0.5775 (m-10) REVERT: E 568 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7371 (mtt180) REVERT: F 33 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6641 (ptt) REVERT: G 81 LEU cc_start: 0.7316 (tp) cc_final: 0.7090 (tt) REVERT: G 123 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7325 (mp) REVERT: H 27 THR cc_start: 0.7061 (p) cc_final: 0.6834 (m) REVERT: I 31 GLN cc_start: 0.7463 (mm-40) cc_final: 0.6947 (mm110) REVERT: I 46 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8375 (m) REVERT: I 66 GLU cc_start: 0.5995 (mt-10) cc_final: 0.5552 (mp0) REVERT: I 227 ILE cc_start: 0.7406 (mt) cc_final: 0.7160 (mt) REVERT: I 420 GLN cc_start: 0.7067 (tp40) cc_final: 0.6661 (tp40) REVERT: I 450 ASN cc_start: 0.6610 (OUTLIER) cc_final: 0.6391 (OUTLIER) REVERT: I 455 ASP cc_start: 0.7686 (t0) cc_final: 0.7432 (t0) REVERT: I 476 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: I 520 MET cc_start: 0.8440 (tpt) cc_final: 0.8007 (tpt) REVERT: I 568 ARG cc_start: 0.7770 (mtt-85) cc_final: 0.7229 (mtt-85) REVERT: I 572 ASN cc_start: 0.7066 (t0) cc_final: 0.6718 (t0) REVERT: J 2 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6337 (ptm-80) REVERT: J 67 MET cc_start: 0.6987 (mtm) cc_final: 0.6686 (mtm) REVERT: J 235 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6724 (mm110) REVERT: K 101 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: L 6 SER cc_start: 0.7896 (OUTLIER) cc_final: 0.7602 (p) REVERT: L 56 PHE cc_start: 0.7544 (t80) cc_final: 0.5340 (m-80) outliers start: 84 outliers final: 26 residues processed: 560 average time/residue: 0.5635 time to fit residues: 363.4898 Evaluate side-chains 534 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 493 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 124 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN E 452 ASN F 235 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 GLN I 367 GLN I 448 ASN J 71 ASN J 109 GLN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.158661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141851 restraints weight = 30772.552| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.08 r_work: 0.3646 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.301 23420 Z= 0.230 Angle : 1.416 84.528 31845 Z= 0.462 Chirality : 0.060 1.382 3507 Planarity : 0.005 0.048 4029 Dihedral : 8.157 78.655 3433 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.86 % Allowed : 17.76 % Favored : 77.39 % 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: -0.32 (0.16), residues: 2841 helix: 1.53 (0.13), residues: 1434 sheet: -2.14 (0.31), residues: 189 loop : -2.12 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 21 TYR 0.034 0.002 TYR L 45 PHE 0.023 0.002 PHE L 60 TRP 0.024 0.002 TRP D 113 HIS 0.008 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00525 (23385) covalent geometry : angle 1.14722 (31770) hydrogen bonds : bond 0.05528 ( 1221) hydrogen bonds : angle 4.65034 ( 3519) metal coordination : bond 0.01238 ( 30) metal coordination : angle 17.15225 ( 75) Misc. bond : bond 0.17543 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 506 time to evaluate : 0.722 Fit side-chains REVERT: A 31 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6699 (mp10) REVERT: A 374 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8290 (ttmp) REVERT: A 438 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: A 476 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6707 (mt-10) REVERT: A 490 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6819 (mp) REVERT: A 568 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7229 (mtt180) REVERT: B 2 ARG cc_start: 0.6690 (ptm160) cc_final: 0.6001 (ptm160) REVERT: B 9 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7516 (mmm-85) REVERT: B 33 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6783 (ptt) REVERT: B 56 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7916 (ttp-170) REVERT: B 136 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7756 (mmm) REVERT: C 71 LYS cc_start: 0.6531 (mmtm) cc_final: 0.6293 (mmtm) REVERT: C 101 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: C 123 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7199 (mp) REVERT: D 6 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7671 (t) REVERT: D 27 THR cc_start: 0.6966 (p) cc_final: 0.6542 (m) REVERT: E 46 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8208 (m) REVERT: E 50 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: E 62 GLU cc_start: 0.7085 (tt0) cc_final: 0.6588 (pt0) REVERT: E 196 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7071 (mtp180) REVERT: E 210 GLN cc_start: 0.6870 (tt0) cc_final: 0.6366 (mt0) REVERT: E 227 ILE cc_start: 0.7526 (mt) cc_final: 0.7303 (mt) REVERT: E 438 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: E 449 ASN cc_start: 0.6406 (m-40) cc_final: 0.6135 (m-40) REVERT: E 455 ASP cc_start: 0.7598 (t0) cc_final: 0.7304 (t0) REVERT: E 545 PHE cc_start: 0.6097 (m-80) cc_final: 0.5624 (m-10) REVERT: E 568 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7378 (mtt180) REVERT: F 33 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6740 (ptt) REVERT: F 142 LYS cc_start: 0.7154 (mmtp) cc_final: 0.6782 (mppt) REVERT: F 168 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7721 (mttt) REVERT: F 235 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: G 53 SER cc_start: 0.7840 (t) cc_final: 0.7078 (p) REVERT: G 119 VAL cc_start: 0.8322 (t) cc_final: 0.8097 (t) REVERT: G 123 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7353 (mp) REVERT: H 56 PHE cc_start: 0.7478 (t80) cc_final: 0.5150 (m-80) REVERT: I 31 GLN cc_start: 0.7478 (mm-40) cc_final: 0.6985 (mm110) REVERT: I 66 GLU cc_start: 0.6161 (mt-10) cc_final: 0.5693 (mp0) REVERT: I 156 ASN cc_start: 0.6874 (m110) cc_final: 0.6517 (m110) REVERT: I 227 ILE cc_start: 0.7476 (mt) cc_final: 0.7262 (mt) REVERT: I 367 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6261 (mt0) REVERT: I 420 GLN cc_start: 0.7035 (tp40) cc_final: 0.6639 (tp40) REVERT: I 455 ASP cc_start: 0.7727 (t0) cc_final: 0.7489 (t0) REVERT: I 471 PHE cc_start: 0.7128 (m-80) cc_final: 0.6905 (m-80) REVERT: I 476 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: I 480 MET cc_start: 0.7622 (mtm) cc_final: 0.7273 (mtt) REVERT: I 490 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6401 (mp) REVERT: I 520 MET cc_start: 0.8387 (tpt) cc_final: 0.8020 (tpt) REVERT: I 572 ASN cc_start: 0.7150 (t0) cc_final: 0.6723 (t0) REVERT: J 2 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6272 (ptm-80) REVERT: J 235 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6786 (mm110) REVERT: K 92 MET cc_start: 0.7767 (mtm) cc_final: 0.7446 (mmm) REVERT: K 101 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: L 56 PHE cc_start: 0.7610 (t80) cc_final: 0.5489 (m-80) outliers start: 116 outliers final: 47 residues processed: 560 average time/residue: 0.5741 time to fit residues: 370.6734 Evaluate side-chains 558 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 492 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 367 GLN Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 262 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 252 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 260 optimal weight: 0.0050 chunk 12 optimal weight: 9.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 452 ASN B 71 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 496 ASN F 71 ASN F 235 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS I 64 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147293 restraints weight = 29971.263| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.14 r_work: 0.3749 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 23420 Z= 0.146 Angle : 1.306 84.322 31845 Z= 0.426 Chirality : 0.058 1.434 3507 Planarity : 0.004 0.050 4029 Dihedral : 7.521 79.457 3431 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.06 % Allowed : 21.06 % Favored : 75.88 % 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: 0.15 (0.16), residues: 2841 helix: 1.94 (0.14), residues: 1437 sheet: -2.01 (0.31), residues: 225 loop : -1.90 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 451 TYR 0.031 0.001 TYR L 45 PHE 0.017 0.001 PHE A 471 TRP 0.025 0.001 TRP H 113 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00305 (23385) covalent geometry : angle 1.09603 (31770) hydrogen bonds : bond 0.04479 ( 1221) hydrogen bonds : angle 4.43536 ( 3519) metal coordination : bond 0.00677 ( 30) metal coordination : angle 14.67270 ( 75) Misc. bond : bond 0.06120 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 512 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6714 (mp10) REVERT: A 168 ASP cc_start: 0.7672 (m-30) cc_final: 0.7290 (t0) REVERT: A 228 ARG cc_start: 0.7473 (mtt90) cc_final: 0.7265 (mtt-85) REVERT: A 438 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6817 (tp30) REVERT: A 476 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6580 (mt-10) REVERT: A 568 ARG cc_start: 0.7620 (mtt180) cc_final: 0.7231 (mtt180) REVERT: B 2 ARG cc_start: 0.6690 (ptm160) cc_final: 0.6062 (ptm160) REVERT: B 9 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: B 33 MET cc_start: 0.7140 (ptm) cc_final: 0.6737 (ptt) REVERT: B 136 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7716 (mmm) REVERT: B 144 ASP cc_start: 0.7986 (m-30) cc_final: 0.7587 (m-30) REVERT: C 71 LYS cc_start: 0.6636 (mmtm) cc_final: 0.6335 (mmtm) REVERT: C 101 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: C 123 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7464 (mm) REVERT: D 6 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7656 (t) REVERT: D 27 THR cc_start: 0.6964 (p) cc_final: 0.6510 (m) REVERT: E 46 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8165 (m) REVERT: E 50 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: E 102 MET cc_start: 0.7044 (mtm) cc_final: 0.6811 (mtm) REVERT: E 210 GLN cc_start: 0.6801 (tt0) cc_final: 0.6397 (mt0) REVERT: E 227 ILE cc_start: 0.7567 (mt) cc_final: 0.7353 (mt) REVERT: E 357 MET cc_start: 0.6386 (mmm) cc_final: 0.6041 (mmm) REVERT: E 405 LEU cc_start: 0.6869 (mm) cc_final: 0.6442 (mt) REVERT: E 438 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7099 (tp30) REVERT: E 455 ASP cc_start: 0.7567 (t0) cc_final: 0.7255 (t0) REVERT: E 568 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7396 (mtt180) REVERT: E 574 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6662 (pp20) REVERT: F 2 ARG cc_start: 0.7093 (ttt90) cc_final: 0.6876 (ttt90) REVERT: F 33 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6635 (ptt) REVERT: F 142 LYS cc_start: 0.7134 (mmtp) cc_final: 0.6808 (mppt) REVERT: F 235 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.7007 (mm110) REVERT: G 53 SER cc_start: 0.7791 (t) cc_final: 0.7147 (p) REVERT: G 93 MET cc_start: 0.7251 (mtp) cc_final: 0.7004 (mtm) REVERT: I 64 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6640 (p0) REVERT: I 66 GLU cc_start: 0.6087 (mt-10) cc_final: 0.5676 (mp0) REVERT: I 227 ILE cc_start: 0.7581 (mt) cc_final: 0.7365 (mt) REVERT: I 420 GLN cc_start: 0.7062 (tp40) cc_final: 0.6699 (tp-100) REVERT: I 438 GLU cc_start: 0.6873 (tp30) cc_final: 0.6553 (tp30) REVERT: I 450 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6380 (t0) REVERT: I 455 ASP cc_start: 0.7689 (t0) cc_final: 0.7322 (t0) REVERT: I 471 PHE cc_start: 0.6799 (m-80) cc_final: 0.6543 (m-80) REVERT: I 476 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: I 480 MET cc_start: 0.7451 (mtm) cc_final: 0.7232 (mtp) REVERT: I 520 MET cc_start: 0.8478 (tpt) cc_final: 0.8111 (tpt) REVERT: I 568 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7340 (mtt180) REVERT: I 572 ASN cc_start: 0.7148 (t0) cc_final: 0.6696 (t0) REVERT: I 574 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6681 (pp20) REVERT: J 2 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6170 (ttt90) REVERT: J 9 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7252 (mmm-85) REVERT: J 102 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7424 (t70) REVERT: J 136 MET cc_start: 0.8251 (mmp) cc_final: 0.8048 (mmp) REVERT: J 235 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6860 (mm110) REVERT: K 92 MET cc_start: 0.7762 (mtm) cc_final: 0.7491 (mmm) REVERT: L 6 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7308 (t) REVERT: L 56 PHE cc_start: 0.7453 (t80) cc_final: 0.5288 (m-80) outliers start: 73 outliers final: 27 residues processed: 544 average time/residue: 0.5654 time to fit residues: 354.4466 Evaluate side-chains 531 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 487 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 71 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 GLN E 452 ASN F 71 ASN F 235 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 448 ASN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.161422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144062 restraints weight = 30276.071| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.16 r_work: 0.3715 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 23420 Z= 0.208 Angle : 1.369 84.656 31845 Z= 0.451 Chirality : 0.059 1.411 3507 Planarity : 0.005 0.064 4029 Dihedral : 7.665 78.834 3428 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.10 % Allowed : 21.40 % Favored : 74.50 % 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: 0.01 (0.16), residues: 2841 helix: 1.79 (0.13), residues: 1437 sheet: -1.81 (0.31), residues: 219 loop : -1.99 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 578 TYR 0.035 0.002 TYR L 45 PHE 0.024 0.002 PHE L 52 TRP 0.025 0.002 TRP D 113 HIS 0.006 0.001 HIS I 143 Details of bonding type rmsd covalent geometry : bond 0.00473 (23385) covalent geometry : angle 1.14380 (31770) hydrogen bonds : bond 0.05176 ( 1221) hydrogen bonds : angle 4.54358 ( 3519) metal coordination : bond 0.01119 ( 30) metal coordination : angle 15.54184 ( 75) Misc. bond : bond 0.10042 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 494 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7385 (mm-40) cc_final: 0.6706 (mp10) REVERT: A 196 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6846 (mtp180) REVERT: A 438 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: A 476 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6791 (mt-10) REVERT: A 490 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6801 (mp) REVERT: A 568 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7275 (mtt180) REVERT: B 2 ARG cc_start: 0.6648 (ptm160) cc_final: 0.6000 (ptm160) REVERT: B 9 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7417 (mmm-85) REVERT: B 33 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6790 (ptt) REVERT: B 136 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7794 (mmm) REVERT: C 53 SER cc_start: 0.7849 (t) cc_final: 0.7229 (p) REVERT: C 71 LYS cc_start: 0.6567 (mmtm) cc_final: 0.6299 (mmtm) REVERT: C 101 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: C 123 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7181 (mp) REVERT: D 6 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7691 (t) REVERT: D 27 THR cc_start: 0.6931 (p) cc_final: 0.6518 (m) REVERT: E 46 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8305 (m) REVERT: E 50 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: E 62 GLU cc_start: 0.7129 (tt0) cc_final: 0.6666 (pt0) REVERT: E 210 GLN cc_start: 0.6924 (tt0) cc_final: 0.6485 (mt0) REVERT: E 227 ILE cc_start: 0.7622 (mt) cc_final: 0.7404 (mt) REVERT: E 438 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: E 568 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7428 (mtt180) REVERT: E 572 ASN cc_start: 0.7251 (t0) cc_final: 0.6995 (t0) REVERT: E 574 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6786 (pp20) REVERT: F 33 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6723 (ptt) REVERT: F 142 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6833 (mppt) REVERT: F 168 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7713 (mttt) REVERT: F 235 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: G 53 SER cc_start: 0.7828 (t) cc_final: 0.7231 (p) REVERT: G 93 MET cc_start: 0.7293 (mtp) cc_final: 0.7035 (mtm) REVERT: G 123 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7264 (mp) REVERT: I 66 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5799 (mp0) REVERT: I 156 ASN cc_start: 0.7038 (m110) cc_final: 0.6673 (m110) REVERT: I 420 GLN cc_start: 0.7084 (tp40) cc_final: 0.6793 (tp-100) REVERT: I 438 GLU cc_start: 0.6950 (tp30) cc_final: 0.6578 (mm-30) REVERT: I 455 ASP cc_start: 0.7702 (t0) cc_final: 0.7441 (t0) REVERT: I 471 PHE cc_start: 0.7056 (m-80) cc_final: 0.6837 (m-80) REVERT: I 476 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: I 490 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6429 (mp) REVERT: I 496 ASN cc_start: 0.7034 (t0) cc_final: 0.6732 (t0) REVERT: I 520 MET cc_start: 0.8438 (tpt) cc_final: 0.8017 (tpt) REVERT: I 568 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7422 (mtt-85) REVERT: I 574 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6746 (pp20) REVERT: J 2 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6130 (ttt90) REVERT: J 235 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6874 (mm110) REVERT: K 92 MET cc_start: 0.7829 (mtm) cc_final: 0.7615 (mmm) REVERT: K 93 MET cc_start: 0.7702 (mtp) cc_final: 0.7278 (OUTLIER) REVERT: K 101 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: L 6 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7521 (t) REVERT: L 56 PHE cc_start: 0.7591 (t80) cc_final: 0.5495 (m-80) outliers start: 98 outliers final: 47 residues processed: 539 average time/residue: 0.5654 time to fit residues: 351.3299 Evaluate side-chains 553 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 486 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 31 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 496 ASN B 71 ASN B 228 HIS B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN G 12 ASN I 64 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 452 ASN I 531 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140367 restraints weight = 30678.703| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.06 r_work: 0.3633 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.255 23420 Z= 0.290 Angle : 1.470 84.939 31845 Z= 0.495 Chirality : 0.062 1.375 3507 Planarity : 0.006 0.065 4029 Dihedral : 8.325 78.614 3428 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.19 % Allowed : 20.85 % Favored : 73.95 % 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: -0.50 (0.15), residues: 2841 helix: 1.26 (0.13), residues: 1455 sheet: -1.79 (0.31), residues: 219 loop : -2.16 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 578 TYR 0.035 0.003 TYR L 45 PHE 0.031 0.002 PHE L 52 TRP 0.028 0.003 TRP D 113 HIS 0.007 0.002 HIS E 45 Details of bonding type rmsd covalent geometry : bond 0.00669 (23385) covalent geometry : angle 1.21168 (31770) hydrogen bonds : bond 0.06136 ( 1221) hydrogen bonds : angle 4.82722 ( 3519) metal coordination : bond 0.01571 ( 30) metal coordination : angle 17.17663 ( 75) Misc. bond : bond 0.14284 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 496 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7406 (mm-40) cc_final: 0.6643 (mp10) REVERT: A 374 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8391 (ttmp) REVERT: A 476 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6850 (mt-10) REVERT: A 490 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6861 (mp) REVERT: A 568 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7216 (mtt-85) REVERT: B 2 ARG cc_start: 0.6700 (ptm160) cc_final: 0.6092 (ptm160) REVERT: B 33 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6856 (ptt) REVERT: B 136 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7820 (mmm) REVERT: C 53 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7263 (p) REVERT: C 71 LYS cc_start: 0.6514 (mmtm) cc_final: 0.6265 (mmtm) REVERT: C 123 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7227 (mp) REVERT: D 27 THR cc_start: 0.6989 (p) cc_final: 0.6618 (m) REVERT: D 77 TRP cc_start: 0.7839 (t60) cc_final: 0.7167 (t-100) REVERT: E 50 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: E 62 GLU cc_start: 0.7156 (tt0) cc_final: 0.6295 (pm20) REVERT: E 65 TRP cc_start: 0.6260 (p-90) cc_final: 0.5964 (p-90) REVERT: E 210 GLN cc_start: 0.7001 (tt0) cc_final: 0.6537 (mt0) REVERT: E 430 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.7137 (ttp80) REVERT: E 449 ASN cc_start: 0.6389 (m-40) cc_final: 0.6054 (m-40) REVERT: E 568 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7408 (mtt180) REVERT: E 572 ASN cc_start: 0.7302 (t0) cc_final: 0.7016 (t0) REVERT: F 2 ARG cc_start: 0.7023 (ttt90) cc_final: 0.6795 (ttt90) REVERT: F 33 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6706 (ptt) REVERT: F 142 LYS cc_start: 0.7131 (mmtp) cc_final: 0.6366 (mppt) REVERT: F 168 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7715 (mtmt) REVERT: F 235 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: G 46 TRP cc_start: 0.7314 (t60) cc_final: 0.6992 (t60) REVERT: G 65 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7069 (tpt) REVERT: G 93 MET cc_start: 0.7336 (mtp) cc_final: 0.7042 (mtm) REVERT: G 123 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7377 (mp) REVERT: H 56 PHE cc_start: 0.7395 (t80) cc_final: 0.5117 (m-80) REVERT: I 31 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6933 (mm110) REVERT: I 64 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6642 (p0) REVERT: I 65 TRP cc_start: 0.6109 (p-90) cc_final: 0.5713 (p-90) REVERT: I 66 GLU cc_start: 0.6111 (mt-10) cc_final: 0.5638 (mp0) REVERT: I 196 ARG cc_start: 0.7304 (mtp85) cc_final: 0.6938 (mtp85) REVERT: I 210 GLN cc_start: 0.6767 (tt0) cc_final: 0.6499 (tt0) REVERT: I 367 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6514 (mt0) REVERT: I 373 GLU cc_start: 0.8226 (pt0) cc_final: 0.7904 (pm20) REVERT: I 420 GLN cc_start: 0.7074 (tp40) cc_final: 0.6740 (tp40) REVERT: I 455 ASP cc_start: 0.7825 (t0) cc_final: 0.7477 (t0) REVERT: I 476 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: I 490 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6463 (mp) REVERT: I 520 MET cc_start: 0.8357 (tpt) cc_final: 0.8146 (tpt) REVERT: I 568 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7523 (mtt-85) REVERT: I 584 LYS cc_start: 0.6220 (mtpp) cc_final: 0.5771 (mmmm) REVERT: J 2 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6004 (ttt90) REVERT: J 9 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7149 (mmm-85) REVERT: J 33 MET cc_start: 0.7213 (ptp) cc_final: 0.6880 (ptt) REVERT: J 102 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7027 (t70) REVERT: J 235 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6721 (mm110) REVERT: K 29 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7797 (mt) REVERT: K 53 SER cc_start: 0.8063 (t) cc_final: 0.7476 (p) REVERT: K 92 MET cc_start: 0.7733 (mtm) cc_final: 0.7459 (mmm) REVERT: K 93 MET cc_start: 0.7681 (mtp) cc_final: 0.7232 (OUTLIER) REVERT: K 101 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: L 6 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7586 (t) REVERT: L 56 PHE cc_start: 0.7546 (t80) cc_final: 0.5484 (m-80) outliers start: 124 outliers final: 67 residues processed: 557 average time/residue: 0.5625 time to fit residues: 361.0915 Evaluate side-chains 560 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 472 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 367 GLN Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 6 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 189 optimal weight: 30.0000 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 0.0570 chunk 171 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 235 GLN F 237 ASN I 64 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.159401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142561 restraints weight = 30156.767| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.07 r_work: 0.3655 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 23420 Z= 0.193 Angle : 1.381 84.763 31845 Z= 0.460 Chirality : 0.060 1.408 3507 Planarity : 0.005 0.052 4029 Dihedral : 7.993 79.034 3428 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.10 % Allowed : 22.19 % Favored : 73.70 % 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: -0.17 (0.16), residues: 2841 helix: 1.59 (0.13), residues: 1437 sheet: -1.69 (0.32), residues: 219 loop : -2.04 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 578 TYR 0.036 0.002 TYR H 45 PHE 0.024 0.002 PHE L 60 TRP 0.029 0.002 TRP D 113 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00431 (23385) covalent geometry : angle 1.15570 (31770) hydrogen bonds : bond 0.05366 ( 1221) hydrogen bonds : angle 4.68241 ( 3519) metal coordination : bond 0.01126 ( 30) metal coordination : angle 15.62774 ( 75) Misc. bond : bond 0.11837 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 490 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7389 (mm-40) cc_final: 0.6576 (mp10) REVERT: A 374 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8316 (ttmp) REVERT: A 430 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7279 (mtm110) REVERT: A 476 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6706 (mt-10) REVERT: A 490 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6666 (mp) REVERT: A 568 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7097 (mtt-85) REVERT: B 2 ARG cc_start: 0.6652 (ptm160) cc_final: 0.5953 (ptm160) REVERT: B 33 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6907 (ptt) REVERT: B 136 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7800 (mmm) REVERT: C 53 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7227 (p) REVERT: C 93 MET cc_start: 0.7216 (mtp) cc_final: 0.6800 (mtt) REVERT: C 123 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7385 (mm) REVERT: D 27 THR cc_start: 0.6938 (p) cc_final: 0.6546 (m) REVERT: D 77 TRP cc_start: 0.7954 (t60) cc_final: 0.7137 (t-100) REVERT: E 46 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8293 (m) REVERT: E 50 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: E 62 GLU cc_start: 0.7076 (tt0) cc_final: 0.6273 (pm20) REVERT: E 210 GLN cc_start: 0.6923 (tt0) cc_final: 0.6480 (mt0) REVERT: E 405 LEU cc_start: 0.6816 (mm) cc_final: 0.6357 (mt) REVERT: E 449 ASN cc_start: 0.6316 (m-40) cc_final: 0.5927 (m-40) REVERT: E 545 PHE cc_start: 0.5902 (m-80) cc_final: 0.5523 (m-10) REVERT: E 568 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7362 (mtt180) REVERT: E 572 ASN cc_start: 0.7311 (t0) cc_final: 0.6984 (t0) REVERT: E 574 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6780 (pp20) REVERT: F 2 ARG cc_start: 0.7061 (ttt90) cc_final: 0.6854 (ttt90) REVERT: F 33 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6711 (ptt) REVERT: F 142 LYS cc_start: 0.7116 (mmtp) cc_final: 0.6740 (mppt) REVERT: F 168 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7673 (mtmt) REVERT: F 235 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: G 46 TRP cc_start: 0.7290 (t60) cc_final: 0.6974 (t60) REVERT: G 53 SER cc_start: 0.7868 (t) cc_final: 0.7205 (p) REVERT: G 65 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7202 (tpt) REVERT: G 93 MET cc_start: 0.7238 (mtp) cc_final: 0.6963 (mtm) REVERT: H 56 PHE cc_start: 0.7397 (t80) cc_final: 0.5091 (m-80) REVERT: I 66 GLU cc_start: 0.6084 (mt-10) cc_final: 0.5695 (mp0) REVERT: I 130 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6103 (tp-100) REVERT: I 210 GLN cc_start: 0.6674 (tt0) cc_final: 0.6398 (tt0) REVERT: I 373 GLU cc_start: 0.8236 (pt0) cc_final: 0.7985 (pm20) REVERT: I 374 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8384 (ttmt) REVERT: I 455 ASP cc_start: 0.7729 (t0) cc_final: 0.7349 (t0) REVERT: I 480 MET cc_start: 0.8038 (mtp) cc_final: 0.7754 (mtm) REVERT: I 490 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6393 (mp) REVERT: I 520 MET cc_start: 0.8366 (tpt) cc_final: 0.8136 (tpt) REVERT: I 531 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7763 (m-40) REVERT: I 568 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7457 (mtt180) REVERT: I 574 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: I 584 LYS cc_start: 0.6291 (mtpp) cc_final: 0.5806 (mmmm) REVERT: J 2 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6082 (ttt90) REVERT: J 9 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7250 (mmm-85) REVERT: J 235 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6718 (mm110) REVERT: K 29 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7747 (mt) REVERT: K 92 MET cc_start: 0.7723 (mtm) cc_final: 0.7484 (mmm) REVERT: K 93 MET cc_start: 0.7644 (mtp) cc_final: 0.7222 (ptp) REVERT: K 101 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: L 6 SER cc_start: 0.7824 (OUTLIER) cc_final: 0.7481 (t) REVERT: L 56 PHE cc_start: 0.7530 (t80) cc_final: 0.5424 (m-80) outliers start: 98 outliers final: 49 residues processed: 537 average time/residue: 0.5755 time to fit residues: 355.6622 Evaluate side-chains 546 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 475 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 374 LYS Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 195 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 chunk 260 optimal weight: 8.9990 chunk 271 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 overall best weight: 7.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 235 GLN F 237 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 452 ASN I 531 ASN J 71 ASN J 123 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140267 restraints weight = 30671.944| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.08 r_work: 0.3633 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.263 23420 Z= 0.290 Angle : 1.473 85.140 31845 Z= 0.502 Chirality : 0.063 1.390 3507 Planarity : 0.006 0.059 4029 Dihedral : 8.391 79.398 3428 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.44 % Allowed : 22.15 % Favored : 73.41 % 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: -0.60 (0.15), residues: 2841 helix: 1.14 (0.13), residues: 1455 sheet: -1.70 (0.32), residues: 219 loop : -2.20 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 578 TYR 0.040 0.003 TYR H 45 PHE 0.030 0.002 PHE D 60 TRP 0.027 0.003 TRP D 113 HIS 0.007 0.002 HIS E 45 Details of bonding type rmsd covalent geometry : bond 0.00673 (23385) covalent geometry : angle 1.22235 (31770) hydrogen bonds : bond 0.06175 ( 1221) hydrogen bonds : angle 4.89248 ( 3519) metal coordination : bond 0.01603 ( 30) metal coordination : angle 16.96883 ( 75) Misc. bond : bond 0.15278 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 482 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6959 (mtp180) REVERT: A 210 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6330 (mt0) REVERT: A 374 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8334 (ttmp) REVERT: A 476 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6883 (mt-10) REVERT: A 490 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6892 (mp) REVERT: A 506 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: A 568 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7220 (mtt-85) REVERT: B 2 ARG cc_start: 0.6688 (ptm160) cc_final: 0.6137 (ptm160) REVERT: B 33 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6980 (ptt) REVERT: B 136 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7815 (mmm) REVERT: C 53 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7226 (p) REVERT: C 71 LYS cc_start: 0.6449 (mptp) cc_final: 0.6239 (mmtm) REVERT: C 101 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: D 27 THR cc_start: 0.6924 (p) cc_final: 0.6563 (m) REVERT: D 77 TRP cc_start: 0.7837 (t60) cc_final: 0.7167 (t-100) REVERT: E 50 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: E 62 GLU cc_start: 0.7084 (tt0) cc_final: 0.6217 (pm20) REVERT: E 65 TRP cc_start: 0.6280 (p-90) cc_final: 0.5996 (p-90) REVERT: E 163 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: E 196 ARG cc_start: 0.7319 (mtp85) cc_final: 0.6987 (mtm180) REVERT: E 210 GLN cc_start: 0.7043 (tt0) cc_final: 0.6603 (mt0) REVERT: E 449 ASN cc_start: 0.6357 (m-40) cc_final: 0.6041 (m-40) REVERT: E 545 PHE cc_start: 0.5964 (m-80) cc_final: 0.5590 (m-10) REVERT: E 568 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7426 (mtt180) REVERT: E 572 ASN cc_start: 0.7283 (t0) cc_final: 0.6967 (t0) REVERT: E 574 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6841 (pp20) REVERT: F 33 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6724 (ptt) REVERT: F 142 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6399 (mppt) REVERT: F 168 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7701 (mtmt) REVERT: F 235 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: G 46 TRP cc_start: 0.7325 (t60) cc_final: 0.7030 (t60) REVERT: G 65 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7109 (tpt) REVERT: G 93 MET cc_start: 0.7322 (mtp) cc_final: 0.7019 (mtm) REVERT: G 119 VAL cc_start: 0.8306 (t) cc_final: 0.8106 (t) REVERT: G 123 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7348 (mp) REVERT: H 56 PHE cc_start: 0.7322 (t80) cc_final: 0.5056 (m-80) REVERT: I 66 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5784 (mp0) REVERT: I 196 ARG cc_start: 0.7338 (mtp85) cc_final: 0.6980 (mtp85) REVERT: I 210 GLN cc_start: 0.6811 (tt0) cc_final: 0.6597 (tt0) REVERT: I 367 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6453 (mt0) REVERT: I 373 GLU cc_start: 0.8291 (pt0) cc_final: 0.8034 (pm20) REVERT: I 455 ASP cc_start: 0.7774 (t0) cc_final: 0.7417 (t0) REVERT: I 490 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6570 (mp) REVERT: I 520 MET cc_start: 0.8308 (tpt) cc_final: 0.8066 (tpt) REVERT: I 531 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7741 (m-40) REVERT: I 568 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7499 (mtt-85) REVERT: I 574 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6795 (pp20) REVERT: I 584 LYS cc_start: 0.6317 (mtpp) cc_final: 0.5647 (mmmt) REVERT: J 2 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5974 (ttt90) REVERT: J 9 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7135 (mmm-85) REVERT: J 33 MET cc_start: 0.7227 (ptp) cc_final: 0.6910 (ptt) REVERT: J 102 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.6931 (t70) REVERT: J 235 GLN cc_start: 0.6968 (mm-40) cc_final: 0.6735 (mm110) REVERT: K 29 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7739 (mt) REVERT: K 53 SER cc_start: 0.8065 (t) cc_final: 0.7463 (p) REVERT: K 92 MET cc_start: 0.7731 (mtm) cc_final: 0.7465 (mmm) REVERT: K 93 MET cc_start: 0.7721 (mtp) cc_final: 0.7276 (ptp) REVERT: K 101 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: L 6 SER cc_start: 0.7887 (OUTLIER) cc_final: 0.7487 (t) REVERT: L 56 PHE cc_start: 0.7630 (t80) cc_final: 0.5596 (m-80) outliers start: 106 outliers final: 56 residues processed: 533 average time/residue: 0.5661 time to fit residues: 347.5637 Evaluate side-chains 550 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 468 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 367 GLN Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 237 optimal weight: 0.0070 chunk 263 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140876 restraints weight = 30766.690| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.07 r_work: 0.3637 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 23420 Z= 0.272 Angle : 1.537 85.026 31845 Z= 0.572 Chirality : 0.061 1.380 3507 Planarity : 0.007 0.150 4029 Dihedral : 8.330 79.546 3426 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.02 % Allowed : 22.53 % Favored : 73.45 % Cbeta Deviations : 0.04 % 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: -0.60 (0.15), residues: 2841 helix: 1.15 (0.13), residues: 1455 sheet: -1.71 (0.32), residues: 219 loop : -2.20 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 578 TYR 0.036 0.003 TYR H 45 PHE 0.024 0.002 PHE D 60 TRP 0.028 0.002 TRP D 113 HIS 0.007 0.001 HIS E 45 Details of bonding type rmsd covalent geometry : bond 0.00611 (23385) covalent geometry : angle 1.30103 (31770) hydrogen bonds : bond 0.06050 ( 1221) hydrogen bonds : angle 4.88925 ( 3519) metal coordination : bond 0.01427 ( 30) metal coordination : angle 16.92712 ( 75) Misc. bond : bond 0.14258 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 471 time to evaluate : 0.756 Fit side-chains REVERT: A 196 ARG cc_start: 0.7154 (mtp85) cc_final: 0.6936 (mtp180) REVERT: A 374 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8328 (ttmp) REVERT: A 476 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6866 (mt-10) REVERT: A 490 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6865 (mp) REVERT: A 568 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7211 (mtt-85) REVERT: B 2 ARG cc_start: 0.6679 (ptm160) cc_final: 0.6126 (ptm160) REVERT: B 33 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6956 (ptt) REVERT: B 136 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7813 (mmm) REVERT: C 53 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7208 (p) REVERT: C 71 LYS cc_start: 0.6448 (mptp) cc_final: 0.6227 (mmtm) REVERT: C 101 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: D 27 THR cc_start: 0.6922 (p) cc_final: 0.6560 (m) REVERT: D 77 TRP cc_start: 0.7826 (t60) cc_final: 0.7151 (t-100) REVERT: E 28 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6975 (tm-30) REVERT: E 50 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: E 62 GLU cc_start: 0.7071 (tt0) cc_final: 0.6206 (pm20) REVERT: E 65 TRP cc_start: 0.6257 (p-90) cc_final: 0.5968 (p-90) REVERT: E 163 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: E 196 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6962 (mtm180) REVERT: E 210 GLN cc_start: 0.7014 (tt0) cc_final: 0.6568 (mt0) REVERT: E 449 ASN cc_start: 0.6344 (m-40) cc_final: 0.6028 (m-40) REVERT: E 545 PHE cc_start: 0.5962 (m-80) cc_final: 0.5589 (m-10) REVERT: E 568 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7411 (mtt180) REVERT: E 572 ASN cc_start: 0.7268 (t0) cc_final: 0.6963 (t0) REVERT: E 574 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6835 (pp20) REVERT: F 33 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6706 (ptt) REVERT: F 142 LYS cc_start: 0.7137 (mmtp) cc_final: 0.6387 (mppt) REVERT: F 168 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7698 (mtmt) REVERT: F 235 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6851 (mm110) REVERT: G 46 TRP cc_start: 0.7319 (t60) cc_final: 0.7010 (t60) REVERT: G 65 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7081 (tpt) REVERT: G 93 MET cc_start: 0.7321 (mtp) cc_final: 0.7017 (mtm) REVERT: G 119 VAL cc_start: 0.8311 (t) cc_final: 0.8068 (t) REVERT: G 123 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7394 (mp) REVERT: H 56 PHE cc_start: 0.7294 (t80) cc_final: 0.5049 (m-80) REVERT: H 60 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7563 (t80) REVERT: I 31 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6634 (mm110) REVERT: I 196 ARG cc_start: 0.7304 (mtp85) cc_final: 0.6946 (mtp85) REVERT: I 210 GLN cc_start: 0.6786 (tt0) cc_final: 0.6573 (tt0) REVERT: I 373 GLU cc_start: 0.8296 (pt0) cc_final: 0.8029 (pm20) REVERT: I 455 ASP cc_start: 0.7764 (t0) cc_final: 0.7408 (t0) REVERT: I 490 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6552 (mp) REVERT: I 520 MET cc_start: 0.8287 (tpt) cc_final: 0.8045 (tpt) REVERT: I 568 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7517 (mtt180) REVERT: I 574 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6779 (pp20) REVERT: I 584 LYS cc_start: 0.6302 (mtpp) cc_final: 0.5633 (mmmt) REVERT: J 2 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6235 (ttt180) REVERT: J 9 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7247 (mmm-85) REVERT: J 33 MET cc_start: 0.7235 (ptp) cc_final: 0.6918 (ptt) REVERT: J 235 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6719 (mm110) REVERT: K 29 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7727 (mt) REVERT: K 53 SER cc_start: 0.8050 (t) cc_final: 0.7445 (p) REVERT: K 92 MET cc_start: 0.7730 (mtm) cc_final: 0.7476 (mmm) REVERT: K 93 MET cc_start: 0.7712 (mtp) cc_final: 0.7250 (ptp) REVERT: K 101 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: L 6 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7476 (t) REVERT: L 56 PHE cc_start: 0.7621 (t80) cc_final: 0.5582 (m-80) outliers start: 96 outliers final: 61 residues processed: 520 average time/residue: 0.5637 time to fit residues: 337.6542 Evaluate side-chains 551 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 466 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 113 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN ** I 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN J 123 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140837 restraints weight = 30561.491| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.06 r_work: 0.3639 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 23420 Z= 0.272 Angle : 1.538 85.026 31845 Z= 0.572 Chirality : 0.061 1.380 3507 Planarity : 0.007 0.150 4029 Dihedral : 8.330 79.546 3426 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.64 % Allowed : 23.07 % Favored : 73.28 % Cbeta Deviations : 0.04 % 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: -0.60 (0.15), residues: 2841 helix: 1.15 (0.13), residues: 1455 sheet: -1.71 (0.32), residues: 219 loop : -2.20 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 578 TYR 0.036 0.003 TYR H 45 PHE 0.024 0.002 PHE D 60 TRP 0.028 0.002 TRP D 113 HIS 0.007 0.001 HIS E 45 Details of bonding type rmsd covalent geometry : bond 0.00611 (23385) covalent geometry : angle 1.30102 (31770) hydrogen bonds : bond 0.06050 ( 1221) hydrogen bonds : angle 4.88925 ( 3519) metal coordination : bond 0.01496 ( 30) metal coordination : angle 16.93243 ( 75) Misc. bond : bond 0.14258 ( 5) =============================================================================== Job complete usr+sys time: 9539.06 seconds wall clock time: 162 minutes 35.15 seconds (9755.15 seconds total)