Starting phenix.real_space_refine (version: dev) on Tue Dec 20 14:56:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7v_14538/12_2022/7z7v_14538_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7v_14538/12_2022/7z7v_14538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7v_14538/12_2022/7z7v_14538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7v_14538/12_2022/7z7v_14538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7v_14538/12_2022/7z7v_14538_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7v_14538/12_2022/7z7v_14538_updated.pdb" } resolution = 2.29 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= 0.025 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 36": "OE1" <-> "OE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G GLU 23": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G GLU 252": "OE1" <-> "OE2" Residue "G ASP 279": "OD1" <-> "OD2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G GLU 349": "OE1" <-> "OE2" Residue "G GLU 684": "OE1" <-> "OE2" Residue "G TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 789": "OE1" <-> "OE2" Residue "G GLU 877": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C ASP 462": "OD1" <-> "OD2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 162": "OD1" <-> "OD2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 178": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "L ASP 51": "OD1" <-> "OD2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 400": "OD1" <-> "OD2" Residue "L GLU 401": "OE1" <-> "OE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 484": "OE1" <-> "OE2" Residue "L ASP 546": "OD1" <-> "OD2" Residue "M ASP 135": "OD1" <-> "OD2" Residue "M PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 62": "OD1" <-> "OD2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 324": "OE1" <-> "OE2" Residue "K PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 39106 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: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4739 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 36, '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: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2544 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 307} Chain: "A" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'3PE': 1, 'C14': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "G" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 374 Classifications: {'water': 374} Link IDs: {None: 373} Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "M" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "K" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 71.753 59.429 190.607 1.00 10.59 S ATOM 2741 SG CYS F 357 75.166 58.851 194.926 1.00 14.52 S ATOM 3062 SG CYS F 398 69.352 55.472 195.437 1.00 13.88 S ATOM 2697 SG CYS F 351 73.808 53.023 191.808 1.00 10.92 S ATOM 4054 SG CYS E 92 82.241 51.041 211.539 1.00 25.54 S ATOM 4088 SG CYS E 97 82.422 51.635 215.035 1.00 25.17 S ATOM 4366 SG CYS E 133 77.020 50.435 211.204 1.00 24.06 S ATOM 4392 SG CYS E 137 76.216 51.120 214.410 1.00 27.51 S ATOM 5476 SG CYS G 114 82.160 65.592 173.117 1.00 6.97 S ATOM 5416 SG CYS G 105 87.394 69.435 174.625 1.00 8.64 S ATOM 5436 SG CYS G 108 88.084 63.362 172.468 1.00 7.80 S ATOM 5830 SG CYS G 156 76.438 57.807 178.031 1.00 10.63 S ATOM 5811 SG CYS G 153 82.288 56.614 181.072 1.00 5.16 S ATOM 5859 SG CYS G 159 79.434 52.126 177.434 1.00 7.28 S ATOM 6207 SG CYS G 203 81.495 57.308 174.373 1.00 25.66 S ATOM 6432 SG CYS G 230 78.189 49.027 153.199 1.00 17.55 S ATOM 6717 SG CYS G 265 78.089 45.164 158.494 1.00 11.97 S ATOM 6480 SG CYS G 237 72.808 48.663 156.330 1.00 16.45 S ATOM 6456 SG CYS G 233 75.039 43.341 153.193 1.00 20.81 S ATOM 4877 SG CYS G 36 69.939 58.750 180.890 1.00 9.54 S ATOM 4953 SG CYS G 47 71.584 62.139 181.258 1.00 9.54 S ATOM 4979 SG CYS G 50 65.842 63.831 181.095 1.00 12.55 S ATOM 5128 SG CYS G 69 65.248 60.283 180.730 1.00 13.56 S ATOM 17239 SG CYS B 129 92.330 92.840 149.583 1.00 17.15 S ATOM 16736 SG CYS B 64 97.575 96.626 151.122 1.00 12.09 S ATOM 16730 SG CYS B 63 92.000 98.680 153.046 1.00 12.79 S ATOM 17456 SG CYS B 158 94.176 92.762 155.231 1.00 11.08 S ATOM 18787 SG CYS I 102 92.985 86.937 161.295 1.00 11.95 S ATOM 18762 SG CYS I 99 98.492 85.662 157.637 1.00 11.64 S ATOM 18805 SG CYS I 105 96.998 82.327 163.033 1.00 14.73 S ATOM 18520 SG CYS I 70 93.101 81.722 157.838 1.00 12.01 S ATOM 18834 SG CYS I 109 97.990 76.801 169.253 1.00 7.72 S ATOM 18497 SG CYS I 66 96.041 76.117 163.128 1.00 10.18 S ATOM 18457 SG CYS I 60 100.143 71.783 165.326 1.00 8.11 S ATOM 18475 SG CYS I 63 93.870 72.375 167.862 1.00 11.14 S Time building chain proxies: 20.90, per 1000 atoms: 0.53 Number of scatterers: 39106 At special positions: 0 Unit cell: (157, 214.5, 241.5, 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 15 15.00 O 7932 8.00 N 6229 7.00 C 24630 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: 17.17 Conformation dependent library (CDL) restraints added in 5.2 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 133 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 50 " 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=" FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" FE3 SF4 F 501 " - pdb=" SG CYS F 398 " 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=" FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" FE2 SF4 G1002 " - pdb=" SG CYS G 153 " 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 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 203 helices and 27 sheets defined 55.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 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 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 276 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' 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: 3.840A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.926A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.826A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.058A 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 157 through 163 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 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 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' 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 409 removed outlier: 4.576A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 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 559 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' 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 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.992A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.598A 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 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 831 through 836 removed outlier: 3.988A pdb=" N SER G 835 " --> pdb=" O VAL G 832 " (cutoff:3.500A) 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: 5.334A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.781A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.903A 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 201 through 204 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 274 removed outlier: 3.595A pdb=" N ARG C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 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: 4.008A 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 591 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 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 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: 3.736A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.783A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.312A 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: 4.415A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.918A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.015A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.509A pdb=" N GLN H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) 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 214 through 217 No H-bonds generated for 'chain 'H' and resid 214 through 217' Processing helix chain 'H' and resid 231 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 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 119 removed outlier: 3.547A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 5.045A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.502A pdb=" N LEU L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.624A 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 230 Processing helix chain 'L' and resid 239 through 244 removed outlier: 5.007A 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 261 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 300 removed outlier: 4.036A 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 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 470 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 548 removed outlier: 6.180A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.578A 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 585 Proline residue: L 572 - end of helix removed outlier: 3.726A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 23 Proline residue: M 10 - end of helix removed outlier: 3.914A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 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 157 removed outlier: 4.717A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.293A 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 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 219 through 234 Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.106A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 removed outlier: 3.578A pdb=" N GLY M 261 " --> pdb=" O VAL M 257 " (cutoff:3.500A) 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 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.762A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.857A 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 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' 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 443 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 502 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: 4.473A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.259A 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: 4.201A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 120 removed outlier: 3.683A 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: 4.276A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.977A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 359 through 362 No H-bonds generated for 'chain 'N' and resid 359 through 362' 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: 4.276A 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 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'J' and resid 3 through 21 removed outlier: 3.543A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) 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 80 through 84 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 113 removed outlier: 5.439A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.772A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) 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: 6.554A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.619A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= D, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= E, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.532A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.408A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.465A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.335A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.839A 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: 6.316A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 901 through 903 Processing sheet with id= N, first strand: chain 'G' and resid 842 through 844 Processing sheet with id= O, first strand: chain 'G' and resid 859 through 863 Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.242A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.711A 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: 6.441A 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 220 removed outlier: 3.538A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.490A 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 3 through 6 Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.385A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.337A 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: 4.053A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.759A 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: 6.963A 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: 6.886A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 61 through 63 1893 hydrogen bonds defined for protein. 5355 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: 15.41 Time building geometry restraints manager: 18.18 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: 16038 1.42 - 1.64: 22208 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38747 Sorted by residual: bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" O13 3PE N 602 " pdb=" P 3PE N 602 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" O13 3PE M1003 " pdb=" P 3PE M1003 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" O13 3PE H 403 " pdb=" P 3PE H 403 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" O13 3PE H 401 " pdb=" P 3PE H 401 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 38742 not shown) Histogram of bond angle deviations from ideal: 68.72 - 82.06: 88 82.06 - 95.40: 0 95.40 - 108.73: 2364 108.73 - 122.07: 43228 122.07 - 135.41: 6838 Bond angle restraints: 52518 Sorted by residual: angle pdb=" CG1 ILE M 109 " pdb=" CB ILE M 109 " pdb=" CG2 ILE M 109 " ideal model delta sigma weight residual 110.70 96.52 14.18 3.00e+00 1.11e-01 2.24e+01 angle pdb=" S3 SF4 F 501 " pdb=" FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.61 -6.51 1.50e+00 4.44e-01 1.88e+01 angle pdb=" CA TYR M 435 " pdb=" CB TYR M 435 " pdb=" CG TYR M 435 " ideal model delta sigma weight residual 113.90 121.57 -7.67 1.80e+00 3.09e-01 1.82e+01 angle pdb=" S3 SF4 F 501 " pdb=" FE2 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.29 -6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" CA LEU N 313 " pdb=" CB LEU N 313 " pdb=" CG LEU N 313 " ideal model delta sigma weight residual 116.30 130.24 -13.94 3.50e+00 8.16e-02 1.59e+01 ... (remaining 52513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 21881 34.41 - 68.82: 782 68.82 - 103.24: 61 103.24 - 137.65: 0 137.65 - 172.06: 1 Dihedral angle restraints: 22725 sinusoidal: 9164 harmonic: 13561 Sorted by residual: 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 85.53 172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA ILE E 145 " pdb=" C ILE E 145 " pdb=" N ASP E 146 " pdb=" CA ASP E 146 " ideal model delta harmonic sigma weight residual -180.00 -148.55 -31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA PRO N 387 " pdb=" C PRO N 387 " pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta harmonic sigma weight residual -180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 22722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.249: 5810 4.249 - 8.499: 0 8.499 - 12.748: 0 12.748 - 16.998: 0 16.998 - 21.247: 28 Chirality restraints: 5838 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 10.69 -21.25 2.00e-01 2.50e+01 1.13e+04 chirality pdb=" FE1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " pdb=" S4 SF4 G1002 " both_signs ideal model delta sigma weight residual False -10.55 10.65 -21.20 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 -10.64 21.20 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5835 not shown) Planarity restraints: 6551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 89 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO J 90 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO J 90 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO J 90 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO G 764 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 357 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C CYS F 357 " -0.044 2.00e-02 2.50e+03 pdb=" O CYS F 357 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG F 358 " 0.015 2.00e-02 2.50e+03 ... (remaining 6548 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 8544 2.77 - 3.31: 37615 3.31 - 3.84: 77653 3.84 - 4.37: 93451 4.37 - 4.90: 149821 Nonbonded interactions: 367084 Sorted by model distance: nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASN G 768 " pdb=" O HOH G1101 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.250 2.440 nonbonded pdb=" O ALA N 312 " pdb=" OG SER N 322 " model vdw 2.262 2.440 nonbonded pdb=" OD1 ASP A 124 " pdb=" O HOH A 301 " model vdw 2.263 2.440 ... (remaining 367079 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 267 5.16 5 C 24630 2.51 5 N 6229 2.21 5 O 7932 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: 2.450 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: 17.930 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.310 Process input model: 105.790 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9262 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 : 0.005 0.077 38747 Z= 0.353 Angle : 0.756 14.183 52518 Z= 0.392 Chirality : 1.465 21.247 5838 Planarity : 0.006 0.106 6551 Dihedral : 16.700 172.059 14051 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.25 (0.11), residues: 4710 helix: 0.66 (0.09), residues: 2718 sheet: -0.13 (0.28), residues: 311 loop : -0.41 (0.15), residues: 1681 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 558 time to evaluate : 4.948 Fit side-chains outliers start: 65 outliers final: 41 residues processed: 609 average time/residue: 1.6159 time to fit residues: 1189.3986 Evaluate side-chains 555 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 514 time to evaluate : 4.445 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 37 residues processed: 4 average time/residue: 0.3639 time to fit residues: 8.5271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 396 optimal weight: 8.9990 chunk 355 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 367 optimal weight: 40.0000 chunk 142 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 425 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 46 GLN E 98 HIS ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN ** G 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN H 138 ASN H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS K 27 ASN K 82 GLN J 22 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9257 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.254 38747 Z= 0.784 Angle : 2.175 50.751 52518 Z= 1.427 Chirality : 0.456 6.858 5838 Planarity : 0.005 0.074 6551 Dihedral : 7.896 174.495 5635 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.00 (0.12), residues: 4710 helix: 1.27 (0.10), residues: 2706 sheet: 0.02 (0.28), residues: 310 loop : -0.06 (0.15), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 524 time to evaluate : 4.731 Fit side-chains outliers start: 133 outliers final: 64 residues processed: 609 average time/residue: 1.6330 time to fit residues: 1201.2993 Evaluate side-chains 587 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 523 time to evaluate : 4.624 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 50 residues processed: 16 average time/residue: 0.7944 time to fit residues: 23.8900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 236 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 290 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 426 optimal weight: 0.9990 chunk 460 optimal weight: 8.9990 chunk 379 optimal weight: 2.9990 chunk 423 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 342 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 845 ASN ** G 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN M 64 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS N 404 GLN K 27 ASN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9239 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.243 38747 Z= 0.734 Angle : 2.161 50.772 52518 Z= 1.423 Chirality : 0.448 6.633 5838 Planarity : 0.004 0.055 6551 Dihedral : 7.741 172.959 5635 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.07 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.29 (0.12), residues: 4710 helix: 1.56 (0.10), residues: 2699 sheet: 0.07 (0.29), residues: 310 loop : -0.02 (0.15), residues: 1701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 540 time to evaluate : 4.433 Fit side-chains outliers start: 119 outliers final: 69 residues processed: 622 average time/residue: 1.6100 time to fit residues: 1212.9887 Evaluate side-chains 592 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 523 time to evaluate : 4.609 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 54 residues processed: 17 average time/residue: 0.7314 time to fit residues: 24.8535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 421 optimal weight: 8.9990 chunk 320 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 428 optimal weight: 5.9990 chunk 453 optimal weight: 0.6980 chunk 223 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 834 GLN G 845 ASN ** G 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS N 404 GLN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9240 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.243 38747 Z= 0.735 Angle : 2.161 50.713 52518 Z= 1.423 Chirality : 0.447 6.597 5838 Planarity : 0.004 0.051 6551 Dihedral : 7.754 173.134 5635 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.42 (0.12), residues: 4710 helix: 1.68 (0.10), residues: 2688 sheet: 0.09 (0.29), residues: 312 loop : 0.02 (0.15), residues: 1710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 532 time to evaluate : 4.466 Fit side-chains revert: symmetry clash outliers start: 130 outliers final: 67 residues processed: 615 average time/residue: 1.6451 time to fit residues: 1225.1891 Evaluate side-chains 592 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 525 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 55 residues processed: 13 average time/residue: 0.6978 time to fit residues: 19.3404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 377 optimal weight: 8.9990 chunk 257 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 187 optimal weight: 0.0170 chunk 386 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 406 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 overall best weight: 3.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN F 238 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS ** N 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9241 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.242 38747 Z= 0.736 Angle : 2.162 50.684 52518 Z= 1.424 Chirality : 0.446 6.582 5838 Planarity : 0.004 0.049 6551 Dihedral : 7.767 173.089 5635 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.47 (0.12), residues: 4710 helix: 1.72 (0.10), residues: 2683 sheet: 0.11 (0.29), residues: 312 loop : 0.06 (0.15), residues: 1715 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 530 time to evaluate : 4.471 Fit side-chains revert: symmetry clash outliers start: 120 outliers final: 71 residues processed: 614 average time/residue: 1.6738 time to fit residues: 1249.5223 Evaluate side-chains 592 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 521 time to evaluate : 4.561 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 58 residues processed: 14 average time/residue: 1.0025 time to fit residues: 26.2431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 152 optimal weight: 5.9990 chunk 408 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 453 optimal weight: 0.9980 chunk 376 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 150 optimal weight: 0.0870 chunk 238 optimal weight: 9.9990 overall best weight: 3.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN F 238 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS ** N 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9236 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.243 38747 Z= 0.731 Angle : 2.160 50.683 52518 Z= 1.423 Chirality : 0.446 6.555 5838 Planarity : 0.004 0.050 6551 Dihedral : 7.734 172.824 5635 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.51 (0.12), residues: 4710 helix: 1.75 (0.10), residues: 2684 sheet: 0.11 (0.29), residues: 312 loop : 0.07 (0.15), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 524 time to evaluate : 4.501 Fit side-chains revert: symmetry clash outliers start: 109 outliers final: 68 residues processed: 598 average time/residue: 1.6840 time to fit residues: 1221.6200 Evaluate side-chains 588 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 520 time to evaluate : 4.509 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 57 residues processed: 12 average time/residue: 0.6904 time to fit residues: 18.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 437 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 452 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN F 238 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS ** N 404 GLN ** 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: 0.9252 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.243 38747 Z= 0.754 Angle : 2.169 50.649 52518 Z= 1.426 Chirality : 0.449 6.631 5838 Planarity : 0.004 0.050 6551 Dihedral : 8.024 173.890 5635 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.44 (0.12), residues: 4710 helix: 1.68 (0.10), residues: 2685 sheet: 0.10 (0.29), residues: 312 loop : 0.08 (0.15), residues: 1713 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 530 time to evaluate : 4.759 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 65 residues processed: 605 average time/residue: 1.7256 time to fit residues: 1265.7742 Evaluate side-chains 589 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 524 time to evaluate : 4.744 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 55 residues processed: 11 average time/residue: 0.6008 time to fit residues: 17.4409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 279 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 88 optimal weight: 0.0000 chunk 87 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN F 238 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS ** N 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 82 GLN J 75 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9247 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.243 38747 Z= 0.746 Angle : 2.168 50.664 52518 Z= 1.426 Chirality : 0.448 6.619 5838 Planarity : 0.004 0.049 6551 Dihedral : 8.068 173.460 5635 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.00 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.46 (0.12), residues: 4710 helix: 1.70 (0.10), residues: 2684 sheet: 0.10 (0.29), residues: 312 loop : 0.08 (0.15), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 528 time to evaluate : 4.709 Fit side-chains revert: symmetry clash outliers start: 101 outliers final: 66 residues processed: 598 average time/residue: 1.7490 time to fit residues: 1267.7667 Evaluate side-chains 590 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 524 time to evaluate : 4.639 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 56 residues processed: 11 average time/residue: 0.7709 time to fit residues: 18.4400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 411 optimal weight: 8.9990 chunk 433 optimal weight: 8.9990 chunk 395 optimal weight: 9.9990 chunk 421 optimal weight: 7.9990 chunk 432 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 chunk 398 optimal weight: 2.9990 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 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS ** N 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN J 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9254 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.243 38747 Z= 0.755 Angle : 2.172 50.641 52518 Z= 1.427 Chirality : 0.449 6.628 5838 Planarity : 0.004 0.050 6551 Dihedral : 8.242 173.797 5635 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.98 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.43 (0.12), residues: 4710 helix: 1.66 (0.10), residues: 2685 sheet: 0.09 (0.29), residues: 311 loop : 0.08 (0.15), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 532 time to evaluate : 5.107 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 65 residues processed: 595 average time/residue: 1.7865 time to fit residues: 1286.9051 Evaluate side-chains 582 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 517 time to evaluate : 4.467 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 57 residues processed: 10 average time/residue: 0.6576 time to fit residues: 15.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 419 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 445 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 372 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS ** N 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.242 38747 Z= 0.729 Angle : 2.163 50.670 52518 Z= 1.424 Chirality : 0.446 6.554 5838 Planarity : 0.004 0.048 6551 Dihedral : 8.043 172.545 5635 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.98 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.53 (0.12), residues: 4710 helix: 1.76 (0.10), residues: 2683 sheet: 0.11 (0.29), residues: 311 loop : 0.10 (0.15), residues: 1716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 522 time to evaluate : 4.939 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 60 residues processed: 581 average time/residue: 1.7193 time to fit residues: 1206.3812 Evaluate side-chains 577 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 517 time to evaluate : 4.513 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 55 residues processed: 6 average time/residue: 0.4383 time to fit residues: 10.5384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 228 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 343 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 372 optimal weight: 0.0170 chunk 155 optimal weight: 0.0570 chunk 382 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 490 GLN G 834 GLN G 845 ASN ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS H 226 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS N 285 ASN ** N 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.068006 restraints weight = 30794.261| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 0.91 r_work: 0.2745 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.244 38747 Z= 0.719 Angle : 2.158 50.724 52518 Z= 1.423 Chirality : 0.441 6.439 5838 Planarity : 0.004 0.048 6551 Dihedral : 7.661 170.433 5635 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.98 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.66 (0.12), residues: 4710 helix: 1.89 (0.10), residues: 2682 sheet: 0.12 (0.29), residues: 312 loop : 0.13 (0.15), residues: 1716 =============================================================================== Job complete usr+sys time: 18830.31 seconds wall clock time: 330 minutes 57.78 seconds (19857.78 seconds total)