Starting phenix.real_space_refine (version: dev) on Tue Dec 20 15:00:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p64_13217/12_2022/7p64_13217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p64_13217/12_2022/7p64_13217.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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p64_13217/12_2022/7p64_13217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p64_13217/12_2022/7p64_13217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p64_13217/12_2022/7p64_13217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p64_13217/12_2022/7p64_13217_updated.pdb" } 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= 0.005 sd= 0.022 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 GLU 9": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G ASP 306": "OD1" <-> "OD2" Residue "G GLU 332": "OE1" <-> "OE2" Residue "G GLU 336": "OE1" <-> "OE2" Residue "G ASP 438": "OD1" <-> "OD2" Residue "G GLU 874": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 51": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "L TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 241": "OD1" <-> "OD2" Residue "L GLU 359": "OE1" <-> "OE2" Residue "L PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M ASP 135": "OD1" <-> "OD2" Residue "N ASP 100": "OD1" <-> "OD2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N GLU 200": "OE1" <-> "OE2" Residue "N ASP 229": "OD1" <-> "OD2" Residue "K ASP 57": "OD1" <-> "OD2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 38981 Number of models: 1 Model: "" Number of chains: 37 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} 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: 4741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4741 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2474 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4637 Classifications: {'peptide': 606} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 587} 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: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3620 Classifications: {'peptide': 478} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'DCQ': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'3PE': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 203 Unusual residues: {'3PE': 4, 'LFA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'3PE': 6, 'LFA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 308 Classifications: {'water': 308} Link IDs: {None: 307} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "N" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 74.768 60.483 191.847 1.00 24.98 S ATOM 2741 SG CYS F 357 78.331 59.905 196.082 1.00 36.60 S ATOM 3062 SG CYS F 398 72.463 56.706 196.813 1.00 36.25 S ATOM 2697 SG CYS F 351 76.688 54.054 193.052 1.00 27.68 S ATOM 4054 SG CYS E 92 86.138 51.990 212.373 1.00 49.60 S ATOM 4088 SG CYS E 97 86.467 52.779 215.849 1.00 48.93 S ATOM 4366 SG CYS E 133 80.921 51.435 212.287 1.00 61.55 S ATOM 4392 SG CYS E 137 80.270 52.235 215.519 1.00 55.26 S ATOM 5476 SG CYS G 114 84.532 66.081 173.721 1.00 12.78 S ATOM 5416 SG CYS G 105 89.900 69.832 174.931 1.00 22.30 S ATOM 5436 SG CYS G 108 90.372 63.731 172.785 1.00 13.38 S ATOM 5830 SG CYS G 156 78.797 58.403 178.993 1.00 19.56 S ATOM 5811 SG CYS G 153 84.756 57.223 181.848 1.00 15.18 S ATOM 5859 SG CYS G 159 81.699 52.688 178.472 1.00 10.59 S ATOM 6203 SG CYS G 203 83.744 57.824 175.205 1.00 17.86 S ATOM 6428 SG CYS G 230 79.449 49.183 154.321 1.00 17.83 S ATOM 6713 SG CYS G 265 79.571 45.456 159.722 1.00 22.05 S ATOM 6476 SG CYS G 237 74.237 49.006 157.683 1.00 15.82 S ATOM 6452 SG CYS G 233 76.239 43.527 154.696 1.00 18.02 S ATOM 4877 SG CYS G 36 72.526 59.622 182.093 1.00 17.78 S ATOM 4953 SG CYS G 47 74.192 62.990 182.347 1.00 15.20 S ATOM 4979 SG CYS G 50 68.484 64.735 182.485 1.00 24.91 S ATOM 5128 SG CYS G 69 67.813 61.174 182.147 1.00 22.83 S ATOM 17236 SG CYS B 129 94.279 92.696 149.025 1.00 17.56 S ATOM 16733 SG CYS B 64 99.640 96.389 150.368 1.00 20.91 S ATOM 16727 SG CYS B 63 94.173 98.583 152.435 1.00 21.43 S ATOM 17453 SG CYS B 158 96.320 92.688 154.669 1.00 25.28 S ATOM 18784 SG CYS I 102 95.258 86.992 160.916 1.00 12.93 S ATOM 18759 SG CYS I 99 100.546 85.585 157.048 1.00 17.28 S ATOM 18802 SG CYS I 105 99.258 82.363 162.594 1.00 19.91 S ATOM 18517 SG CYS I 70 95.171 81.678 157.588 1.00 18.18 S ATOM 18831 SG CYS I 109 100.424 76.964 168.913 1.00 15.95 S ATOM 18494 SG CYS I 66 98.211 76.194 162.887 1.00 26.03 S ATOM 18454 SG CYS I 60 102.312 71.830 165.027 1.00 20.25 S ATOM 18472 SG CYS I 63 96.179 72.556 167.801 1.00 18.36 S Time building chain proxies: 21.14, per 1000 atoms: 0.54 Number of scatterers: 38981 At special positions: 0 Unit cell: (158.5, 215, 243.5, 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 267 16.00 P 21 15.00 O 7647 8.00 N 6209 7.00 C 24804 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: 17.79 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 97 " 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=" FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" FE2 SF4 B 301 " - pdb=" SG CYS B 64 " 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=" FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" FE1 SF4 G1002 " - pdb=" SG CYS G 156 " 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=" FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 26 sheets defined 55.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 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 56 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 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 274 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 311 through 316 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 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.887A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.757A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.764A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.111A 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 155 through 164 Proline residue: E 159 - end of helix removed outlier: 3.714A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.153A 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 84 through 98 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 123 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 215 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: 4.517A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.670A 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 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: 3.570A 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 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' 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: 4.774A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 768 Processing helix chain 'G' and resid 825 through 829 removed outlier: 4.045A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 825 through 829' Processing helix chain 'G' and resid 831 through 836 removed outlier: 4.382A pdb=" N SER G 835 " --> pdb=" O PRO G 831 " (cutoff:3.500A) removed outlier: 3.874A 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 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.194A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.720A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.557A 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 330 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 376 through 397 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.084A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) 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 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 116 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 178 removed outlier: 3.857A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.803A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 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 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.844A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.966A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.007A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 181 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 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 119 removed outlier: 3.619A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.607A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.513A pdb=" N LEU L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) 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 238 through 244 removed outlier: 5.006A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 258 through 268 removed outlier: 3.621A pdb=" N ALA L 261 " --> pdb=" O MET L 258 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY L 262 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 362 through 364 No H-bonds generated for 'chain 'L' and resid 362 through 364' Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 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 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.127A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 560 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.767A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (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: 3.868A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 85 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.755A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.422A 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 164 through 200 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 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.742A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (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 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 Processing helix chain 'M' and resid 452 through 454 No H-bonds generated for 'chain 'M' and resid 452 through 454' Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 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 58 removed outlier: 4.536A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.133A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 120 removed outlier: 3.638A pdb=" N LEU N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 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: 4.435A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 267 through 288 removed outlier: 3.553A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.752A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.089A 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: 4.136A 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 90 through 112 removed outlier: 5.209A 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 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.632A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.917A 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: 6.611A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.439A 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: 6.509A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.437A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.752A 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: 6.321A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.889A 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 removed outlier: 7.927A pdb=" N TYR G 841 " --> pdb=" O PRO G 887 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 860 through 863 Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.244A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.652A 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: 6.399A 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: 6.560A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.453A 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 539 removed outlier: 3.599A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.388A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= W, first strand: chain 'I' and resid 75 through 81 removed outlier: 4.055A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) 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: 6.948A 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: 6.854A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1886 hydrogen bonds defined for protein. 5325 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: 14.17 Time building geometry restraints manager: 18.69 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: 16008 1.42 - 1.64: 22411 1.64 - 1.86: 410 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38921 Sorted by residual: bond pdb=" CB PRO C 201 " pdb=" CG PRO C 201 " ideal model delta sigma weight residual 1.492 1.684 -0.192 5.00e-02 4.00e+02 1.48e+01 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 8.98e+00 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 8.92e+00 bond pdb=" O13 3PE M 702 " pdb=" P 3PE M 702 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O13 3PE J 201 " pdb=" P 3PE J 201 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.82e+00 ... (remaining 38916 not shown) Histogram of bond angle deviations from ideal: 68.96 - 82.44: 88 82.44 - 95.91: 3 95.91 - 109.39: 3644 109.39 - 122.87: 46263 122.87 - 136.35: 2679 Bond angle restraints: 52677 Sorted by residual: angle pdb=" CA PRO C 201 " pdb=" N PRO C 201 " pdb=" CD PRO C 201 " ideal model delta sigma weight residual 112.00 95.20 16.80 1.40e+00 5.10e-01 1.44e+02 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 95.89 13.92 2.21e+00 2.05e-01 3.97e+01 angle pdb=" N PRO C 201 " pdb=" CD PRO C 201 " pdb=" CG PRO C 201 " ideal model delta sigma weight residual 103.20 94.36 8.84 1.50e+00 4.44e-01 3.47e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 134.65 -12.85 2.44e+00 1.68e-01 2.77e+01 angle pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 ... (remaining 52672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 22143 34.05 - 68.10: 671 68.10 - 102.15: 40 102.15 - 136.21: 0 136.21 - 170.26: 1 Dihedral angle restraints: 22855 sinusoidal: 9342 harmonic: 13513 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 180.00 137.63 42.37 0 5.00e+00 4.00e-02 7.18e+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 87.34 170.26 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.51 34.49 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 22852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5799 4.240 - 8.479: 0 8.479 - 12.719: 0 12.719 - 16.958: 0 16.958 - 21.198: 28 Chirality restraints: 5827 Sorted by residual: chirality pdb=" FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.20 2.00e-01 2.50e+01 1.12e+04 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=" FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.19 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5824 not shown) Planarity restraints: 6534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ B 302 " -0.010 2.00e-02 2.50e+03 3.22e-02 3.11e+01 pdb=" C1M DCQ B 302 " -0.074 2.00e-02 2.50e+03 pdb=" C2 DCQ B 302 " 0.007 2.00e-02 2.50e+03 pdb=" C3 DCQ B 302 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DCQ B 302 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DCQ B 302 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DCQ B 302 " 0.036 2.00e-02 2.50e+03 pdb=" C7 DCQ B 302 " 0.051 2.00e-02 2.50e+03 pdb=" O2 DCQ B 302 " 0.040 2.00e-02 2.50e+03 pdb=" O3 DCQ B 302 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DCQ B 302 " -0.003 2.00e-02 2.50e+03 pdb=" O5 DCQ B 302 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " -0.086 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO C 201 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL N 63 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.022 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 6531 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6815 2.76 - 3.30: 37182 3.30 - 3.83: 74494 3.83 - 4.37: 91316 4.37 - 4.90: 148346 Nonbonded interactions: 358153 Sorted by model distance: nonbonded pdb=" O HOH G1105 " pdb=" O HOH G1317 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.237 2.440 nonbonded pdb=" OD2 ASP K 57 " pdb=" OH TYR J 137 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.250 2.440 nonbonded pdb=" OE1 GLN C 16 " pdb=" O HOH C 701 " model vdw 2.250 2.440 ... (remaining 358148 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 21 5.49 5 S 267 5.16 5 C 24804 2.51 5 N 6209 2.21 5 O 7647 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: 3.270 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: 18.810 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.380 Process input model: 104.740 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 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 0.192 38921 Z= 0.358 Angle : 0.766 16.804 52677 Z= 0.392 Chirality : 1.466 21.198 5827 Planarity : 0.006 0.117 6534 Dihedral : 15.546 170.257 14213 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % 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: -0.05 (0.11), residues: 4692 helix: 0.51 (0.09), residues: 2693 sheet: -0.44 (0.27), residues: 323 loop : -0.67 (0.14), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 482 time to evaluate : 4.959 Fit side-chains outliers start: 57 outliers final: 40 residues processed: 528 average time/residue: 1.6286 time to fit residues: 1039.8040 Evaluate side-chains 507 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 467 time to evaluate : 4.718 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 0.4319 time to fit residues: 7.5109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 424 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 196 ASN F 386 GLN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN E 103 GLN G 57 ASN G 88 GLN G 232 GLN G 583 ASN G 745 GLN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN L 121 ASN L 315 GLN M 45 GLN M 56 GLN N 7 ASN K 5 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.255 38921 Z= 0.730 Angle : 2.165 51.036 52677 Z= 1.425 Chirality : 0.442 6.512 5827 Planarity : 0.005 0.058 6534 Dihedral : 7.972 170.476 5835 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.95 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % 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: 0.83 (0.12), residues: 4692 helix: 1.27 (0.10), residues: 2671 sheet: -0.15 (0.28), residues: 315 loop : -0.35 (0.15), residues: 1706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 489 time to evaluate : 5.099 Fit side-chains outliers start: 121 outliers final: 63 residues processed: 561 average time/residue: 1.5828 time to fit residues: 1079.8578 Evaluate side-chains 534 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 471 time to evaluate : 4.241 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 42 residues processed: 21 average time/residue: 0.7644 time to fit residues: 28.2598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 458 optimal weight: 10.0000 chunk 378 optimal weight: 3.9990 chunk 421 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 340 optimal weight: 6.9990 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 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN F 386 GLN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN G 57 ASN G 88 GLN G 299 GLN G 583 ASN G 655 HIS G 768 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN H 208 HIS ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN M 80 HIS K 5 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.246 38921 Z= 0.787 Angle : 2.176 50.953 52677 Z= 1.427 Chirality : 0.451 6.674 5827 Planarity : 0.005 0.056 6534 Dihedral : 8.711 171.188 5835 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.63 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % 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: 0.89 (0.12), residues: 4692 helix: 1.29 (0.10), residues: 2660 sheet: -0.07 (0.28), residues: 316 loop : -0.26 (0.15), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 465 time to evaluate : 4.460 Fit side-chains outliers start: 120 outliers final: 63 residues processed: 539 average time/residue: 1.6311 time to fit residues: 1070.0801 Evaluate side-chains 520 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 457 time to evaluate : 4.840 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 47 residues processed: 16 average time/residue: 0.8154 time to fit residues: 24.5855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 2.9990 chunk 319 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 285 optimal weight: 0.7980 chunk 426 optimal weight: 1.9990 chunk 451 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 404 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 107 GLN F 386 GLN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN G 88 GLN G 583 ASN G 605 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN K 5 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.252 38921 Z= 0.706 Angle : 2.150 50.940 52677 Z= 1.419 Chirality : 0.440 6.588 5827 Planarity : 0.004 0.061 6534 Dihedral : 7.931 169.735 5835 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.27 (0.12), residues: 4692 helix: 1.68 (0.10), residues: 2671 sheet: -0.13 (0.28), residues: 320 loop : -0.25 (0.15), residues: 1701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 486 time to evaluate : 4.704 Fit side-chains outliers start: 110 outliers final: 58 residues processed: 562 average time/residue: 1.6113 time to fit residues: 1120.0995 Evaluate side-chains 529 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 471 time to evaluate : 4.916 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 47 residues processed: 11 average time/residue: 0.6867 time to fit residues: 17.5651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 385 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 405 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 107 GLN F 386 GLN E 78 GLN G 57 ASN G 88 GLN G 583 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN K 5 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.242 38921 Z= 0.748 Angle : 2.164 50.908 52677 Z= 1.423 Chirality : 0.448 6.678 5827 Planarity : 0.004 0.060 6534 Dihedral : 8.343 170.155 5835 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.68 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % 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: 1.22 (0.12), residues: 4692 helix: 1.59 (0.10), residues: 2670 sheet: -0.02 (0.28), residues: 317 loop : -0.19 (0.15), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 465 time to evaluate : 4.494 Fit side-chains outliers start: 114 outliers final: 64 residues processed: 543 average time/residue: 1.6137 time to fit residues: 1063.7457 Evaluate side-chains 530 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 466 time to evaluate : 4.457 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 50 residues processed: 14 average time/residue: 0.8302 time to fit residues: 22.3984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 3.9990 chunk 406 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 451 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 261 HIS G 583 ASN G 605 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN K 5 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 38921 Z= 0.759 Angle : 2.169 50.957 52677 Z= 1.425 Chirality : 0.448 6.669 5827 Planarity : 0.004 0.058 6534 Dihedral : 8.720 170.618 5835 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.74 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: 1.14 (0.12), residues: 4692 helix: 1.50 (0.10), residues: 2669 sheet: -0.03 (0.28), residues: 317 loop : -0.18 (0.15), residues: 1706 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 467 time to evaluate : 4.576 Fit side-chains outliers start: 107 outliers final: 65 residues processed: 540 average time/residue: 1.6927 time to fit residues: 1108.7361 Evaluate side-chains 528 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 463 time to evaluate : 4.720 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 51 residues processed: 14 average time/residue: 0.6641 time to fit residues: 20.1742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 329 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 380 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 450 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 chunk 274 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN M 56 GLN K 5 GLN K 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.245 38921 Z= 0.716 Angle : 2.157 50.965 52677 Z= 1.421 Chirality : 0.443 6.535 5827 Planarity : 0.004 0.058 6534 Dihedral : 8.396 169.859 5835 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.74 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % 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: 1.33 (0.12), residues: 4692 helix: 1.69 (0.10), residues: 2675 sheet: -0.01 (0.28), residues: 316 loop : -0.17 (0.15), residues: 1701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 473 time to evaluate : 4.533 Fit side-chains outliers start: 96 outliers final: 61 residues processed: 540 average time/residue: 1.6322 time to fit residues: 1072.7932 Evaluate side-chains 531 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 470 time to evaluate : 4.548 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 49 residues processed: 12 average time/residue: 0.8484 time to fit residues: 20.2134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 306 optimal weight: 8.9990 chunk 222 optimal weight: 0.0870 chunk 41 optimal weight: 6.9990 chunk 353 optimal weight: 9.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN K 5 GLN K 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.244 38921 Z= 0.757 Angle : 2.169 50.841 52677 Z= 1.425 Chirality : 0.448 6.648 5827 Planarity : 0.004 0.059 6534 Dihedral : 8.770 170.345 5835 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.59 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % 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: 1.19 (0.12), residues: 4692 helix: 1.55 (0.10), residues: 2670 sheet: -0.04 (0.28), residues: 323 loop : -0.16 (0.15), residues: 1699 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 462 time to evaluate : 5.168 Fit side-chains outliers start: 88 outliers final: 61 residues processed: 524 average time/residue: 1.7205 time to fit residues: 1097.0392 Evaluate side-chains 521 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 460 time to evaluate : 4.645 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 53 residues processed: 9 average time/residue: 0.8101 time to fit residues: 16.4885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 6.9990 chunk 431 optimal weight: 3.9990 chunk 393 optimal weight: 8.9990 chunk 419 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 379 optimal weight: 9.9990 chunk 396 optimal weight: 0.9990 chunk 417 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN K 5 GLN K 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.244 38921 Z= 0.720 Angle : 2.159 50.838 52677 Z= 1.421 Chirality : 0.444 6.514 5827 Planarity : 0.004 0.057 6534 Dihedral : 8.532 169.897 5835 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.74 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % 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: 1.32 (0.12), residues: 4692 helix: 1.68 (0.10), residues: 2666 sheet: 0.02 (0.28), residues: 316 loop : -0.16 (0.15), residues: 1710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 463 time to evaluate : 5.077 Fit side-chains outliers start: 75 outliers final: 55 residues processed: 520 average time/residue: 1.6682 time to fit residues: 1054.2610 Evaluate side-chains 517 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 462 time to evaluate : 4.884 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 49 residues processed: 6 average time/residue: 0.9756 time to fit residues: 14.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 9.9990 chunk 443 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 465 optimal weight: 3.9990 chunk 428 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 286 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 583 ASN G 605 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN M 56 GLN K 5 GLN K 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.249 38921 Z= 0.748 Angle : 2.168 50.889 52677 Z= 1.424 Chirality : 0.448 6.662 5827 Planarity : 0.004 0.059 6534 Dihedral : 8.738 170.168 5835 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.61 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % 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: 1.23 (0.12), residues: 4692 helix: 1.59 (0.10), residues: 2668 sheet: -0.03 (0.28), residues: 323 loop : -0.15 (0.15), residues: 1701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 459 time to evaluate : 4.618 Fit side-chains outliers start: 73 outliers final: 62 residues processed: 519 average time/residue: 1.7293 time to fit residues: 1091.6397 Evaluate side-chains 521 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 459 time to evaluate : 4.542 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 54 residues processed: 9 average time/residue: 0.9551 time to fit residues: 17.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 371 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 381 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 386 GLN G 88 GLN G 583 ASN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN K 5 GLN K 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.065346 restraints weight = 38416.478| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.04 r_work: 0.2739 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.246 38921 Z= 0.748 Angle : 2.168 50.920 52677 Z= 1.424 Chirality : 0.448 6.654 5827 Planarity : 0.004 0.057 6534 Dihedral : 8.848 170.291 5835 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.68 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % 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: 1.21 (0.12), residues: 4692 helix: 1.56 (0.10), residues: 2669 sheet: -0.04 (0.28), residues: 323 loop : -0.16 (0.15), residues: 1700 =============================================================================== Job complete usr+sys time: 25013.92 seconds wall clock time: 437 minutes 54.30 seconds (26274.30 seconds total)