Starting phenix.real_space_refine (version: dev) on Tue Dec 20 07:46:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p69_13222/12_2022/7p69_13222_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p69_13222/12_2022/7p69_13222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p69_13222/12_2022/7p69_13222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p69_13222/12_2022/7p69_13222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p69_13222/12_2022/7p69_13222_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p69_13222/12_2022/7p69_13222_updated.pdb" } resolution = 3.0 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= 0.004 sd= 0.020 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 37577 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4597 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1339 Classifications: {'peptide': 169} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 157} Chain breaks: 2 Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2422 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 796 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4595 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 582} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3635 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "L" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 341 Unusual residues: {'3PE': 6, 'LFA': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 76.148 59.075 197.648 1.00 23.25 S ATOM 2766 SG CYS F 357 79.740 58.726 201.931 1.00 41.84 S ATOM 3087 SG CYS F 398 74.089 55.086 202.563 1.00 29.31 S ATOM 2722 SG CYS F 351 78.534 52.827 198.822 1.00 17.57 S ATOM 4079 SG CYS E 92 88.002 51.072 218.313 1.00 47.18 S ATOM 4113 SG CYS E 97 88.153 51.870 221.755 1.00 41.18 S ATOM 4391 SG CYS E 133 82.823 50.276 218.007 1.00 38.35 S ATOM 4417 SG CYS E 137 82.007 50.965 221.245 1.00 47.14 S ATOM 5501 SG CYS G 114 85.724 65.599 179.734 1.00 15.40 S ATOM 5441 SG CYS G 105 90.786 69.728 181.028 1.00 11.56 S ATOM 5461 SG CYS G 108 91.726 63.722 178.840 1.00 8.68 S ATOM 5855 SG CYS G 156 80.494 57.545 184.886 1.00 11.24 S ATOM 5836 SG CYS G 153 86.476 56.663 187.713 1.00 7.17 S ATOM 5884 SG CYS G 159 83.726 51.987 184.288 1.00 9.55 S ATOM 6228 SG CYS G 203 85.506 57.279 181.093 1.00 3.10 S ATOM 6453 SG CYS G 230 81.954 48.615 160.093 1.00 12.71 S ATOM 6738 SG CYS G 265 82.246 44.835 165.451 1.00 10.51 S ATOM 6501 SG CYS G 237 76.734 48.102 163.418 1.00 14.02 S ATOM 6477 SG CYS G 233 79.056 42.812 160.323 1.00 10.80 S ATOM 4902 SG CYS G 36 74.004 58.213 187.938 1.00 10.53 S ATOM 4978 SG CYS G 47 75.513 61.687 188.172 1.00 8.48 S ATOM 5004 SG CYS G 50 69.713 63.073 188.318 1.00 18.54 S ATOM 5153 SG CYS G 69 69.301 59.468 187.951 1.00 19.72 S ATOM 16888 SG CYS B 129 94.274 93.266 155.492 1.00 40.63 S ATOM 16524 SG CYS B 64 99.323 97.288 156.876 1.00 86.94 S ATOM 16518 SG CYS B 63 93.495 99.049 158.693 1.00 79.18 S ATOM 17105 SG CYS B 158 96.307 93.439 161.181 1.00 54.13 S ATOM 18149 SG CYS I 102 95.274 87.493 167.163 1.00 8.14 S ATOM 18124 SG CYS I 99 100.707 86.324 163.453 1.00 12.95 S ATOM 18167 SG CYS I 105 99.508 83.029 168.946 1.00 11.38 S ATOM 17882 SG CYS I 70 95.553 82.149 163.901 1.00 8.76 S ATOM 18196 SG CYS I 109 100.937 77.618 175.221 1.00 12.77 S ATOM 17859 SG CYS I 66 98.847 76.760 169.170 1.00 11.64 S ATOM 17819 SG CYS I 60 103.226 72.698 171.329 1.00 14.82 S ATOM 17837 SG CYS I 63 97.030 72.922 174.041 1.00 11.28 S Time building chain proxies: 21.99, per 1000 atoms: 0.59 Number of scatterers: 37577 At special positions: 0 Unit cell: (158.5, 210.5, 251.5, 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 32 26.01 Ca 1 19.99 S 264 16.00 P 15 15.00 O 7071 8.00 N 6072 7.00 C 24122 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.87 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb=" FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb=" FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb=" FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 501 " pdb=" FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb=" FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb=" FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb=" FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb=" FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb=" FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb=" FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1003 " pdb=" FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb=" FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb=" FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb=" FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb=" FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb=" FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb=" FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb=" FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 26 sheets defined 54.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 303 through 306 removed outlier: 4.051A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 303 through 306' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.862A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.721A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.137A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 164 removed outlier: 4.920A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 84 through 100 removed outlier: 4.492A pdb=" N ASN G 100 " --> pdb=" O TRP G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.125A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.571A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 604 removed outlier: 3.955A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 604' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 5.057A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 831 through 836 removed outlier: 4.173A pdb=" N SER G 835 " --> pdb=" O PRO G 831 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 831 through 836' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.487A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.755A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.654A pdb=" N MET C 285 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 376 through 398 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 572 through 574 No H-bonds generated for 'chain 'C' and resid 572 through 574' Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 104 through 115 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'H' and resid 6 through 39 Processing helix chain 'H' and resid 56 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.938A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.774A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE H 132 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.085A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 215 through 218 removed outlier: 3.869A pdb=" N GLU H 218 " --> pdb=" O PRO H 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 215 through 218' Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 322 removed outlier: 4.881A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.788A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 241 through 244 removed outlier: 3.840A pdb=" N ALA L 244 " --> pdb=" O ASP L 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 241 through 244' Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 260 through 268 Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'L' and resid 277 through 300 removed outlier: 3.634A pdb=" N LEU L 299 " --> pdb=" O GLY L 295 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL L 300 " --> pdb=" O PHE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 387 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 455 through 464 Processing helix chain 'L' and resid 466 through 469 No H-bonds generated for 'chain 'L' and resid 466 through 469' Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 559 removed outlier: 6.106A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE L 549 " --> pdb=" O ASP L 546 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL L 550 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS L 551 " --> pdb=" O VAL L 548 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 585 Proline residue: L 572 - end of helix removed outlier: 3.813A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 612 Processing helix chain 'M' and resid 3 through 21 Proline residue: M 10 - end of helix removed outlier: 3.809A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 3.719A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 165 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 217 through 234 removed outlier: 3.716A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.203A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 266 through 274 Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 331 removed outlier: 3.641A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 397 removed outlier: 3.608A pdb=" N GLY M 397 " --> pdb=" O VAL M 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 502 removed outlier: 4.859A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 57 Processing helix chain 'N' and resid 71 through 96 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 180 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.457A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.614A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.369A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 111 removed outlier: 5.047A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 Processing sheet with id= A, first strand: chain 'F' and resid 214 through 218 removed outlier: 6.793A pdb=" N TYR F 86 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASN F 217 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU F 88 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU F 87 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY F 128 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS F 89 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE F 130 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA F 91 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU F 132 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.619A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= I, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.468A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 285 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.447A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.342A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 901 through 903 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 7.861A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.328A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.460A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 215 through 219 removed outlier: 3.548A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 531 through 538 Processing sheet with id= T, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.675A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 59 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 97 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= V, first strand: chain 'I' and resid 75 through 77 Processing sheet with id= W, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= X, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 66 removed outlier: 7.071A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.880A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1837 hydrogen bonds defined for protein. 5208 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: 13.19 Time building geometry restraints manager: 17.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15652 1.42 - 1.64: 21757 1.64 - 1.86: 403 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 37904 Sorted by residual: bond pdb=" O13 3PE L 705 " pdb=" P 3PE L 705 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" O13 3PE H 602 " pdb=" P 3PE H 602 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" O13 3PE L 702 " pdb=" P 3PE L 702 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" O13 3PE A 202 " pdb=" P 3PE A 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" O13 3PE A 203 " pdb=" P 3PE A 203 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.69e+00 ... (remaining 37899 not shown) Histogram of bond angle deviations from ideal: 69.14 - 82.34: 88 82.34 - 95.53: 0 95.53 - 108.73: 2377 108.73 - 121.92: 41748 121.92 - 135.12: 7143 Bond angle restraints: 51356 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.10 12.71 2.21e+00 2.05e-01 3.31e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 133.82 -12.02 2.44e+00 1.68e-01 2.43e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" CB THR N 64 " ideal model delta sigma weight residual 110.37 118.44 -8.07 1.78e+00 3.16e-01 2.06e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 129.91 -8.37 1.91e+00 2.74e-01 1.92e+01 angle pdb=" S3 SF4 F 501 " pdb=" FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.12 -6.02 1.50e+00 4.44e-01 1.61e+01 ... (remaining 51351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 21858 34.36 - 68.71: 360 68.71 - 103.07: 18 103.07 - 137.43: 0 137.43 - 171.78: 1 Dihedral angle restraints: 22237 sinusoidal: 8973 harmonic: 13264 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.56 44.44 0 5.00e+00 4.00e-02 7.90e+01 dihedral pdb=" CA ASN G 260 " pdb=" C ASN G 260 " pdb=" N HIS G 261 " pdb=" CA HIS G 261 " ideal model delta harmonic sigma weight residual -180.00 -145.16 -34.84 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 85.81 171.78 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 22234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5686 4.238 - 8.477: 0 8.477 - 12.715: 0 12.715 - 16.953: 0 16.953 - 21.191: 28 Chirality restraints: 5714 Sorted by residual: chirality pdb=" FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5711 not shown) Planarity restraints: 6391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 4 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO N 5 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C VAL N 63 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.021 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 260 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" C ASN G 260 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN G 260 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS G 261 " -0.015 2.00e-02 2.50e+03 ... (remaining 6388 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2270 2.73 - 3.27: 37474 3.27 - 3.82: 68859 3.82 - 4.36: 86935 4.36 - 4.90: 143233 Nonbonded interactions: 338771 Sorted by model distance: nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.188 2.440 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.221 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.260 2.440 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.265 2.440 ... (remaining 338766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 15 5.49 5 S 264 5.16 5 C 24122 2.51 5 N 6072 2.21 5 O 7071 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.060 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: 0.030 Extract box with map and model: 18.050 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.320 Process input model: 105.090 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 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 : 0.006 0.062 37904 Z= 0.403 Angle : 0.730 12.714 51356 Z= 0.380 Chirality : 1.479 21.191 5714 Planarity : 0.006 0.085 6391 Dihedral : 12.702 171.784 13753 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.56 % Favored : 97.41 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4601 helix: 0.35 (0.09), residues: 2663 sheet: -0.36 (0.29), residues: 318 loop : -0.69 (0.15), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 609 time to evaluate : 4.237 Fit side-chains revert: symmetry clash outliers start: 80 outliers final: 19 residues processed: 666 average time/residue: 1.4676 time to fit residues: 1191.2279 Evaluate side-chains 509 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 490 time to evaluate : 4.337 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 4 average time/residue: 0.8101 time to fit residues: 10.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 7.9990 chunk 348 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 360 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 417 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 341 ASN F 386 GLN E 98 HIS G 54 GLN G 57 ASN G 218 ASN G 238 ASN G 583 ASN G 901 HIS C 152 HIS C 317 ASN C 344 GLN B 52 ASN H 113 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 GLN L 360 GLN L 524 ASN N 149 GLN N 199 ASN N 404 GLN K 82 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.255 37904 Z= 0.820 Angle : 2.204 51.044 51356 Z= 1.445 Chirality : 0.454 6.627 5714 Planarity : 0.006 0.074 6391 Dihedral : 7.969 173.370 5554 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.67 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.12), residues: 4601 helix: 0.98 (0.10), residues: 2657 sheet: -0.31 (0.29), residues: 317 loop : -0.42 (0.15), residues: 1627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 499 time to evaluate : 4.471 Fit side-chains revert: symmetry clash outliers start: 112 outliers final: 47 residues processed: 573 average time/residue: 1.5444 time to fit residues: 1076.3932 Evaluate side-chains 519 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 472 time to evaluate : 4.472 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 35 residues processed: 14 average time/residue: 0.7716 time to fit residues: 20.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 418 optimal weight: 10.0000 chunk 452 optimal weight: 9.9990 chunk 372 optimal weight: 0.9980 chunk 414 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 341 ASN F 386 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS G 583 ASN C 344 GLN B 52 ASN B 213 ASN H 113 ASN H 152 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 GLN L 524 ASN N 149 GLN N 199 ASN K 82 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.242 37904 Z= 0.750 Angle : 2.183 50.639 51356 Z= 1.439 Chirality : 0.448 6.531 5714 Planarity : 0.004 0.069 6391 Dihedral : 7.744 172.935 5554 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4601 helix: 1.34 (0.10), residues: 2655 sheet: -0.13 (0.29), residues: 306 loop : -0.34 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 490 time to evaluate : 4.620 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 50 residues processed: 562 average time/residue: 1.5242 time to fit residues: 1044.4258 Evaluate side-chains 517 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 467 time to evaluate : 4.604 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 35 residues processed: 16 average time/residue: 0.7669 time to fit residues: 23.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 281 optimal weight: 0.0040 chunk 419 optimal weight: 5.9990 chunk 444 optimal weight: 10.0000 chunk 219 optimal weight: 30.0000 chunk 398 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 583 ASN C 344 GLN B 52 ASN B 213 ASN H 113 ASN L 28 ASN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.243 37904 Z= 0.741 Angle : 2.177 50.645 51356 Z= 1.436 Chirality : 0.446 6.459 5714 Planarity : 0.004 0.068 6391 Dihedral : 7.480 172.102 5554 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4601 helix: 1.64 (0.10), residues: 2625 sheet: -0.05 (0.29), residues: 309 loop : -0.19 (0.15), residues: 1667 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 498 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 46 residues processed: 573 average time/residue: 1.5479 time to fit residues: 1089.1187 Evaluate side-chains 521 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 475 time to evaluate : 4.498 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 38 residues processed: 10 average time/residue: 0.8733 time to fit residues: 18.1080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 331 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 379 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 227 optimal weight: 0.9990 chunk 399 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS G 583 ASN C 236 GLN C 344 GLN B 52 ASN B 213 ASN H 113 ASN L 58 GLN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 ASN K 82 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.240 37904 Z= 0.791 Angle : 2.198 50.610 51356 Z= 1.444 Chirality : 0.450 6.595 5714 Planarity : 0.005 0.067 6391 Dihedral : 8.188 172.900 5554 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.54 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.12), residues: 4601 helix: 1.46 (0.10), residues: 2650 sheet: -0.15 (0.29), residues: 304 loop : -0.18 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 483 time to evaluate : 4.466 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 52 residues processed: 552 average time/residue: 1.5234 time to fit residues: 1029.2450 Evaluate side-chains 514 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 462 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 39 residues processed: 14 average time/residue: 1.0430 time to fit residues: 25.5663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 9.9990 chunk 400 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 445 optimal weight: 0.9980 chunk 369 optimal weight: 5.9990 chunk 206 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN C 236 GLN C 344 GLN B 52 ASN B 213 ASN H 113 ASN L 58 GLN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 37904 Z= 0.751 Angle : 2.184 50.626 51356 Z= 1.439 Chirality : 0.447 6.494 5714 Planarity : 0.004 0.067 6391 Dihedral : 7.979 172.934 5554 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4601 helix: 1.61 (0.10), residues: 2637 sheet: -0.02 (0.30), residues: 303 loop : -0.15 (0.15), residues: 1661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 474 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 49 residues processed: 540 average time/residue: 1.4793 time to fit residues: 977.8997 Evaluate side-chains 511 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 462 time to evaluate : 4.533 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 42 residues processed: 7 average time/residue: 0.9174 time to fit residues: 14.6408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 443 optimal weight: 0.0870 chunk 277 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 583 ASN C 236 GLN C 344 GLN B 213 ASN H 113 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 ASN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.240 37904 Z= 0.760 Angle : 2.187 50.610 51356 Z= 1.440 Chirality : 0.449 6.531 5714 Planarity : 0.004 0.067 6391 Dihedral : 8.031 172.466 5554 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4601 helix: 1.59 (0.10), residues: 2634 sheet: -0.04 (0.29), residues: 306 loop : -0.13 (0.15), residues: 1661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 470 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 55 residues processed: 540 average time/residue: 1.5871 time to fit residues: 1052.3903 Evaluate side-chains 517 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 462 time to evaluate : 4.648 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 8 average time/residue: 1.0012 time to fit residues: 16.3109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 219 optimal weight: 0.0020 chunk 41 optimal weight: 6.9990 chunk 348 optimal weight: 0.8980 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN C 344 GLN B 213 ASN H 113 ASN L 58 GLN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.242 37904 Z= 0.743 Angle : 2.180 50.624 51356 Z= 1.437 Chirality : 0.446 6.461 5714 Planarity : 0.004 0.067 6391 Dihedral : 7.762 172.175 5554 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 4601 helix: 1.73 (0.10), residues: 2622 sheet: 0.03 (0.29), residues: 309 loop : -0.08 (0.15), residues: 1670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 482 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 56 residues processed: 543 average time/residue: 1.5932 time to fit residues: 1061.9457 Evaluate side-chains 527 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 471 time to evaluate : 4.802 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 47 residues processed: 10 average time/residue: 0.9480 time to fit residues: 19.2815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 1.9990 chunk 424 optimal weight: 6.9990 chunk 387 optimal weight: 10.0000 chunk 413 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 373 optimal weight: 8.9990 chunk 390 optimal weight: 0.9990 chunk 411 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 218 ASN G 583 ASN B 213 ASN H 113 ASN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 ASN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 37904 Z= 0.749 Angle : 2.184 50.617 51356 Z= 1.439 Chirality : 0.447 6.487 5714 Planarity : 0.004 0.067 6391 Dihedral : 7.788 172.083 5554 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 4601 helix: 1.73 (0.10), residues: 2621 sheet: 0.05 (0.30), residues: 302 loop : -0.09 (0.15), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 473 time to evaluate : 4.805 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 54 residues processed: 539 average time/residue: 1.4737 time to fit residues: 972.7413 Evaluate side-chains 524 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 470 time to evaluate : 4.088 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 48 residues processed: 6 average time/residue: 0.7076 time to fit residues: 11.7860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 1.9990 chunk 436 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 458 optimal weight: 5.9990 chunk 421 optimal weight: 2.9990 chunk 364 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 425 GLN G 345 HIS G 583 ASN C 236 GLN C 344 GLN B 213 ASN H 113 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 HIS L 58 GLN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 ASN K 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.240 37904 Z= 0.782 Angle : 2.198 50.594 51356 Z= 1.443 Chirality : 0.451 6.581 5714 Planarity : 0.005 0.067 6391 Dihedral : 8.201 172.769 5554 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.54 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.12), residues: 4601 helix: 1.57 (0.10), residues: 2636 sheet: -0.04 (0.29), residues: 305 loop : -0.12 (0.15), residues: 1660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 466 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 51 residues processed: 521 average time/residue: 1.5872 time to fit residues: 1013.6298 Evaluate side-chains 506 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 455 time to evaluate : 4.866 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 46 residues processed: 5 average time/residue: 0.4759 time to fit residues: 10.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 289 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 336 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 375 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 386 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN H 113 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN L 358 HIS L 360 GLN L 524 ASN ** N 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 ASN N 404 GLN ** K 82 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 = 0.3164 r_free = 0.3164 target = 0.083173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.063569 restraints weight = 46881.847| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.14 r_work: 0.2630 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 37904 Z= 0.753 Angle : 2.189 50.611 51356 Z= 1.440 Chirality : 0.448 6.496 5714 Planarity : 0.004 0.067 6391 Dihedral : 8.029 172.568 5554 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.12), residues: 4601 helix: 1.67 (0.10), residues: 2624 sheet: -0.00 (0.30), residues: 302 loop : -0.10 (0.15), residues: 1675 =============================================================================== Job complete usr+sys time: 27254.29 seconds wall clock time: 476 minutes 3.33 seconds (28563.33 seconds total)