Starting phenix.real_space_refine on Sun Dec 17 00:54:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7j_13237/12_2023/7p7j_13237_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7j_13237/12_2023/7p7j_13237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7j_13237/12_2023/7p7j_13237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7j_13237/12_2023/7p7j_13237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7j_13237/12_2023/7p7j_13237_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7j_13237/12_2023/7p7j_13237_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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 13 5.49 5 S 267 5.16 5 C 24392 2.51 5 N 6169 2.21 5 O 6574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 904": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I ASP 162": "OD1" <-> "OD2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "L ASP 400": "OD1" <-> "OD2" Residue "L PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 246": "OD1" <-> "OD2" Residue "M ASP 370": "OD1" <-> "OD2" Residue "M PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 62": "OD1" <-> "OD2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "N GLU 324": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "J GLU 2": "OE1" <-> "OE2" Residue "J TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 120": "OD1" <-> "OD2" Residue "J TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 37448 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4712 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 546} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1553 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2470 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4563 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} 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: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1199 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'DCQ': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "H" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "L" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 230 Unusual residues: {'3PE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 71.861 60.180 195.159 1.00 24.55 S ATOM 2741 SG CYS F 357 75.323 59.897 199.525 1.00 35.82 S ATOM 3062 SG CYS F 398 69.602 56.378 200.117 1.00 24.99 S ATOM 2697 SG CYS F 351 74.127 53.931 196.544 1.00 30.26 S ATOM 4054 SG CYS E 92 82.759 52.229 216.240 1.00 63.33 S ATOM 4088 SG CYS E 97 82.908 53.057 219.711 1.00 62.82 S ATOM 4366 SG CYS E 133 77.634 51.606 215.849 1.00 72.20 S ATOM 4392 SG CYS E 137 76.762 52.331 219.124 1.00 75.45 S ATOM 5476 SG CYS G 114 82.216 66.267 177.570 1.00 15.77 S ATOM 5416 SG CYS G 105 87.339 70.222 179.098 1.00 27.04 S ATOM 5436 SG CYS G 108 88.241 64.206 176.887 1.00 10.56 S ATOM 5830 SG CYS G 156 76.614 58.302 182.582 1.00 11.61 S ATOM 5811 SG CYS G 153 82.489 57.530 185.704 1.00 9.61 S ATOM 5859 SG CYS G 159 79.823 52.770 182.269 1.00 14.53 S ATOM 6203 SG CYS G 203 81.799 57.982 179.050 1.00 7.25 S ATOM 6428 SG CYS G 230 78.771 49.043 158.108 1.00 15.13 S ATOM 6713 SG CYS G 265 78.784 45.343 163.558 1.00 16.49 S ATOM 6476 SG CYS G 237 73.440 48.669 161.221 1.00 17.22 S ATOM 6452 SG CYS G 233 75.759 43.282 158.353 1.00 20.84 S ATOM 4877 SG CYS G 36 70.150 59.205 185.375 1.00 21.02 S ATOM 4953 SG CYS G 47 71.725 62.551 185.623 1.00 11.90 S ATOM 4979 SG CYS G 50 65.802 64.074 185.501 1.00 21.85 S ATOM 5128 SG CYS G 69 65.536 60.420 185.202 1.00 23.26 S ATOM 17192 SG CYS B 129 91.846 93.190 153.179 1.00 17.49 S ATOM 16689 SG CYS B 64 96.949 97.087 154.735 1.00 18.07 S ATOM 16683 SG CYS B 63 91.382 99.078 156.620 1.00 16.11 S ATOM 17409 SG CYS B 158 93.600 93.281 158.942 1.00 20.57 S ATOM 18740 SG CYS I 102 92.475 87.564 165.200 1.00 13.47 S ATOM 18715 SG CYS I 99 98.040 86.365 161.575 1.00 2.14 S ATOM 18758 SG CYS I 105 96.702 83.162 167.069 1.00 17.38 S ATOM 18473 SG CYS I 70 92.891 82.223 161.900 1.00 3.46 S ATOM 18787 SG CYS I 109 97.820 77.855 173.392 1.00 5.17 S ATOM 18450 SG CYS I 66 95.889 77.007 167.339 1.00 7.30 S ATOM 18410 SG CYS I 60 100.126 72.798 169.686 1.00 14.03 S ATOM 18428 SG CYS I 63 93.818 73.197 172.094 1.00 3.79 S Time building chain proxies: 19.61, per 1000 atoms: 0.52 Number of scatterers: 37448 At special positions: 0 Unit cell: (155.82, 210.94, 246.98, 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 13 15.00 O 6574 8.00 N 6169 7.00 C 24392 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: 14.60 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " 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="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8622 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 195 helices and 26 sheets defined 54.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.32 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 69 through 75 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 236 No H-bonds generated for 'chain 'F' and resid 233 through 236' Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 311 through 317 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 389 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: 4.054A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.773A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.720A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.054A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 155 through 164 removed outlier: 3.536A pdb=" N ILE E 158 " --> pdb=" O PRO E 155 " (cutoff:3.500A) Proline residue: E 159 - end of helix removed outlier: 3.723A pdb=" N LEU E 162 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 164 " --> pdb=" O LEU E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 164' 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 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 273 through 276 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.431A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 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 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.958A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 768 Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 831 through 836 removed outlier: 4.417A pdb=" N SER G 835 " --> pdb=" O PRO G 831 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 831 through 836' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.040A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 59 " --> pdb=" O GLN C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.676A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP C 142 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 274 removed outlier: 3.656A pdb=" N ARG C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.620A pdb=" N MET C 285 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 376 through 397 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 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 115 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.716A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.739A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.289A 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 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' 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: 4.707A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.275A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.775A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.715A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.557A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.552A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.944A 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 214 through 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 4.932A 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 260 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 413 through 437 Processing helix chain 'L' and resid 455 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 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.064A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 560 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.749A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 2 through 23 Proline residue: M 10 - end of helix removed outlier: 3.792A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.558A 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 145 Processing helix chain 'M' and resid 148 through 156 Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 219 through 233 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 267 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.607A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.477A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.252A 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: 4.046A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 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: 4.432A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.581A 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 316 removed outlier: 3.807A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 432 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 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 113 removed outlier: 5.767A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.675A 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: 6.692A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.587A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'G' and resid 172 through 175 Processing sheet with id= I, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.457A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.543A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.248A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 813 through 817 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 7.783A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.201A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.685A 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: 6.494A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 215 through 219 removed outlier: 3.528A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.426A 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: 6.392A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.375A 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: 3.997A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.690A 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: 7.021A 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: 6.898A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1852 hydrogen bonds defined for protein. 5322 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: 12.51 Time building geometry restraints manager: 15.71 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: 15914 1.42 - 1.64: 21961 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38376 Sorted by residual: bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" O13 3PE 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 8.77e+00 bond pdb=" O13 3PE A 202 " pdb=" P 3PE A 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" O13 3PE M 701 " pdb=" P 3PE M 701 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" O13 3PE I 203 " pdb=" P 3PE I 203 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.71e+00 ... (remaining 38371 not shown) Histogram of bond angle deviations from ideal: 68.98 - 82.45: 88 82.45 - 95.91: 1 95.91 - 109.37: 3485 109.37 - 122.83: 45713 122.83 - 136.30: 2753 Bond angle restraints: 52040 Sorted by residual: angle pdb=" CA PRO N 483 " pdb=" N PRO N 483 " pdb=" CD PRO N 483 " ideal model delta sigma weight residual 112.00 99.08 12.92 1.40e+00 5.10e-01 8.51e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.15 12.66 2.21e+00 2.05e-01 3.28e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 126.78 -14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 132.31 -10.51 2.44e+00 1.68e-01 1.86e+01 ... (remaining 52035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 21933 33.84 - 67.68: 641 67.68 - 101.52: 34 101.52 - 135.36: 7 135.36 - 169.20: 1 Dihedral angle restraints: 22616 sinusoidal: 9137 harmonic: 13479 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 134.71 45.29 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 144.66 35.34 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 88.39 169.20 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 22613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5772 4.238 - 8.475: 0 8.475 - 12.713: 0 12.713 - 16.951: 0 16.951 - 21.188: 28 Chirality restraints: 5800 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 10.63 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5797 not shown) Planarity restraints: 6496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ B 302 " -0.004 2.00e-02 2.50e+03 2.38e-02 1.70e+01 pdb=" C1M DCQ B 302 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DCQ B 302 " -0.012 2.00e-02 2.50e+03 pdb=" C3 DCQ B 302 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DCQ B 302 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DCQ B 302 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DCQ B 302 " 0.009 2.00e-02 2.50e+03 pdb=" C7 DCQ B 302 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DCQ B 302 " -0.036 2.00e-02 2.50e+03 pdb=" O3 DCQ B 302 " 0.060 2.00e-02 2.50e+03 pdb=" O4 DCQ B 302 " -0.016 2.00e-02 2.50e+03 pdb=" O5 DCQ B 302 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET N 482 " 0.068 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO N 483 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO N 483 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO N 483 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 86 " -0.296 9.50e-02 1.11e+02 1.33e-01 1.20e+01 pdb=" NE ARG K 86 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG K 86 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG K 86 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG K 86 " -0.004 2.00e-02 2.50e+03 ... (remaining 6493 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4088 2.75 - 3.29: 36624 3.29 - 3.82: 68897 3.82 - 4.36: 83307 4.36 - 4.90: 139845 Nonbonded interactions: 332761 Sorted by model distance: nonbonded pdb=" OE1 GLU H 36 " pdb=" OH TYR H 242 " model vdw 2.212 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR A 116 " pdb=" OE2 GLU N 104 " model vdw 2.269 2.440 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.276 2.440 ... (remaining 332756 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 4.010 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 100.720 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 0.136 38376 Z= 0.331 Angle : 0.769 14.084 52040 Z= 0.394 Chirality : 1.468 21.188 5800 Planarity : 0.006 0.133 6496 Dihedral : 15.312 169.205 13994 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 1.25 % Allowed : 14.71 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 4677 helix: 0.37 (0.09), residues: 2705 sheet: -0.58 (0.29), residues: 298 loop : -0.88 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 53 HIS 0.005 0.001 HIS F 431 PHE 0.037 0.002 PHE L 341 TYR 0.036 0.002 TYR H 242 ARG 0.019 0.001 ARG G 727 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 435 time to evaluate : 4.406 Fit side-chains outliers start: 48 outliers final: 33 residues processed: 476 average time/residue: 1.5767 time to fit residues: 898.3929 Evaluate side-chains 451 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 418 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 3 average time/residue: 0.3617 time to fit residues: 5.8461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 366 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 424 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 88 GLN G 299 GLN G 310 GLN G 490 GLN G 583 ASN G 655 HIS B 116 GLN H 45 ASN H 170 GLN ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 GLN H 312 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 38376 Z= 0.724 Angle : 2.168 50.970 52040 Z= 1.428 Chirality : 0.443 6.552 5800 Planarity : 0.005 0.064 6496 Dihedral : 9.549 168.477 5667 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 2.39 % Allowed : 13.67 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 0.61 (0.12), residues: 4677 helix: 1.17 (0.10), residues: 2683 sheet: -0.45 (0.29), residues: 293 loop : -0.58 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.007 0.001 HIS G 101 PHE 0.028 0.001 PHE L 341 TYR 0.023 0.001 TYR H 242 ARG 0.007 0.000 ARG G 727 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 446 time to evaluate : 4.157 Fit side-chains outliers start: 92 outliers final: 47 residues processed: 512 average time/residue: 1.3740 time to fit residues: 847.5536 Evaluate side-chains 478 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 431 time to evaluate : 2.662 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 39 residues processed: 10 average time/residue: 0.7007 time to fit residues: 12.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 424 optimal weight: 0.5980 chunk 458 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 421 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 490 GLN G 583 ASN C 359 HIS C 487 ASN B 116 GLN H 45 ASN H 170 GLN ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN J 22 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.257 38376 Z= 0.713 Angle : 2.166 50.897 52040 Z= 1.427 Chirality : 0.445 6.558 5800 Planarity : 0.004 0.067 6496 Dihedral : 9.374 167.898 5667 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.65 % Allowed : 13.33 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 0.98 (0.12), residues: 4677 helix: 1.49 (0.10), residues: 2673 sheet: -0.30 (0.29), residues: 284 loop : -0.44 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 PHE 0.027 0.001 PHE L 341 TYR 0.029 0.002 TYR H 242 ARG 0.008 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 442 time to evaluate : 2.550 Fit side-chains outliers start: 102 outliers final: 52 residues processed: 516 average time/residue: 1.4372 time to fit residues: 893.7307 Evaluate side-chains 482 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 430 time to evaluate : 4.136 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 42 residues processed: 12 average time/residue: 0.9030 time to fit residues: 19.8737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 426 optimal weight: 10.0000 chunk 451 optimal weight: 0.9980 chunk 222 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN B 52 ASN H 45 ASN H 170 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.256 38376 Z= 0.739 Angle : 2.175 50.806 52040 Z= 1.431 Chirality : 0.447 6.576 5800 Planarity : 0.004 0.065 6496 Dihedral : 9.358 168.130 5667 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 13.36 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.05 (0.12), residues: 4677 helix: 1.52 (0.10), residues: 2681 sheet: -0.28 (0.29), residues: 292 loop : -0.38 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 143 HIS 0.009 0.001 HIS G 101 PHE 0.026 0.002 PHE L 341 TYR 0.027 0.002 TYR H 242 ARG 0.010 0.001 ARG L 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 430 time to evaluate : 3.258 Fit side-chains outliers start: 101 outliers final: 52 residues processed: 503 average time/residue: 1.4600 time to fit residues: 891.9100 Evaluate side-chains 476 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 424 time to evaluate : 4.147 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 46 residues processed: 7 average time/residue: 1.1113 time to fit residues: 15.6805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 230 optimal weight: 4.9990 chunk 405 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 HIS F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN H 45 ASN H 170 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 38376 Z= 0.734 Angle : 2.175 50.852 52040 Z= 1.431 Chirality : 0.446 6.571 5800 Planarity : 0.004 0.065 6496 Dihedral : 9.256 168.122 5667 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.42 % Allowed : 13.85 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.10 (0.12), residues: 4677 helix: 1.56 (0.10), residues: 2677 sheet: -0.29 (0.29), residues: 295 loop : -0.34 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 PHE 0.026 0.002 PHE L 341 TYR 0.025 0.002 TYR H 242 ARG 0.010 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 436 time to evaluate : 4.220 Fit side-chains outliers start: 93 outliers final: 54 residues processed: 504 average time/residue: 1.6132 time to fit residues: 985.3478 Evaluate side-chains 482 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 428 time to evaluate : 4.545 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 46 residues processed: 9 average time/residue: 1.1396 time to fit residues: 19.1650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 0.5980 chunk 406 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 265 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 451 optimal weight: 0.9990 chunk 375 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN H 45 ASN H 170 GLN ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 285 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.011 0.248 38376 Z= 0.706 Angle : 2.168 51.110 52040 Z= 1.428 Chirality : 0.443 6.598 5800 Planarity : 0.004 0.067 6496 Dihedral : 9.025 167.953 5667 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.23 % Allowed : 14.32 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.27 (0.12), residues: 4677 helix: 1.72 (0.10), residues: 2663 sheet: -0.17 (0.30), residues: 282 loop : -0.30 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 143 HIS 0.007 0.001 HIS G 101 PHE 0.027 0.001 PHE E 126 TYR 0.024 0.001 TYR H 242 ARG 0.012 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 430 time to evaluate : 4.268 Fit side-chains outliers start: 86 outliers final: 50 residues processed: 497 average time/residue: 1.6254 time to fit residues: 979.3591 Evaluate side-chains 471 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 421 time to evaluate : 4.136 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 45 residues processed: 6 average time/residue: 1.2705 time to fit residues: 15.2256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 380 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 450 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 207 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 490 GLN G 583 ASN H 45 ASN H 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 38376 Z= 0.739 Angle : 2.178 50.726 52040 Z= 1.432 Chirality : 0.447 6.571 5800 Planarity : 0.004 0.066 6496 Dihedral : 9.086 168.153 5667 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.31 % Allowed : 14.16 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.19 (0.12), residues: 4677 helix: 1.63 (0.10), residues: 2669 sheet: -0.30 (0.29), residues: 295 loop : -0.28 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.008 0.001 HIS G 101 PHE 0.031 0.002 PHE E 126 TYR 0.024 0.002 TYR N 76 ARG 0.010 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 426 time to evaluate : 4.109 Fit side-chains outliers start: 89 outliers final: 57 residues processed: 493 average time/residue: 1.6818 time to fit residues: 1004.0069 Evaluate side-chains 480 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 423 time to evaluate : 4.550 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 51 residues processed: 8 average time/residue: 1.1253 time to fit residues: 17.6840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 268 optimal weight: 0.0870 chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 286 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 353 optimal weight: 8.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN H 45 ASN H 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38376 Z= 0.718 Angle : 2.175 50.903 52040 Z= 1.431 Chirality : 0.445 6.577 5800 Planarity : 0.004 0.070 6496 Dihedral : 9.021 167.987 5667 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.16 % Allowed : 14.35 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.26 (0.12), residues: 4677 helix: 1.69 (0.10), residues: 2660 sheet: -0.23 (0.30), residues: 289 loop : -0.26 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.007 0.001 HIS G 101 PHE 0.030 0.002 PHE E 126 TYR 0.024 0.002 TYR H 242 ARG 0.016 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 427 time to evaluate : 4.150 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 56 residues processed: 496 average time/residue: 1.6082 time to fit residues: 964.1298 Evaluate side-chains 476 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 420 time to evaluate : 3.914 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 53 residues processed: 5 average time/residue: 1.5355 time to fit residues: 14.3075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 393 optimal weight: 0.1980 chunk 419 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 329 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 379 optimal weight: 0.6980 chunk 396 optimal weight: 9.9990 chunk 417 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN E 119 GLN G 88 GLN G 490 GLN G 583 ASN H 45 ASN H 113 ASN H 170 GLN ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38376 Z= 0.699 Angle : 2.168 50.731 52040 Z= 1.428 Chirality : 0.442 6.496 5800 Planarity : 0.004 0.070 6496 Dihedral : 8.726 167.678 5667 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.72 % Allowed : 15.05 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.42 (0.12), residues: 4677 helix: 1.84 (0.10), residues: 2659 sheet: -0.17 (0.30), residues: 280 loop : -0.22 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.024 0.001 TYR M 435 ARG 0.009 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 438 time to evaluate : 4.775 Fit side-chains outliers start: 66 outliers final: 45 residues processed: 495 average time/residue: 1.6287 time to fit residues: 978.6843 Evaluate side-chains 472 residues out of total 3859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 427 time to evaluate : 4.035 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 42 residues processed: 4 average time/residue: 0.8031 time to fit residues: 9.8354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6148 > 50: distance: 127 - 150: 30.206 distance: 136 - 158: 33.734 distance: 141 - 169: 32.471 distance: 144 - 150: 27.496 distance: 145 - 177: 23.528 distance: 150 - 151: 26.274 distance: 151 - 152: 45.458 distance: 151 - 154: 50.363 distance: 152 - 153: 29.958 distance: 152 - 158: 27.107 distance: 153 - 185: 55.899 distance: 154 - 155: 30.671 distance: 155 - 156: 12.260 distance: 156 - 157: 38.980 distance: 158 - 159: 3.512 distance: 159 - 160: 22.480 distance: 159 - 162: 16.406 distance: 160 - 161: 21.997 distance: 160 - 169: 51.337 distance: 161 - 193: 24.781 distance: 162 - 163: 41.002 distance: 163 - 164: 11.923 distance: 163 - 165: 20.221 distance: 164 - 166: 17.545 distance: 165 - 167: 13.992 distance: 166 - 168: 16.363 distance: 169 - 170: 49.964 distance: 170 - 171: 16.895 distance: 170 - 173: 41.425 distance: 171 - 172: 27.726 distance: 171 - 177: 34.655 distance: 172 - 204: 32.394 distance: 173 - 174: 31.061 distance: 173 - 175: 16.083 distance: 174 - 176: 16.228 distance: 177 - 178: 28.094 distance: 178 - 179: 53.324 distance: 178 - 181: 4.870 distance: 179 - 180: 43.701 distance: 179 - 185: 32.059 distance: 180 - 209: 52.051 distance: 181 - 182: 41.482 distance: 182 - 183: 39.507 distance: 182 - 184: 21.926 distance: 185 - 186: 30.723 distance: 186 - 187: 39.106 distance: 186 - 189: 36.883 distance: 187 - 193: 57.042 distance: 189 - 190: 16.462 distance: 189 - 191: 15.987 distance: 190 - 192: 14.647 distance: 193 - 194: 4.877 distance: 194 - 195: 41.536 distance: 194 - 197: 38.980 distance: 195 - 204: 56.383 distance: 197 - 198: 37.088 distance: 198 - 199: 10.298 distance: 199 - 200: 40.440 distance: 200 - 201: 19.139 distance: 201 - 202: 33.065 distance: 201 - 203: 38.078 distance: 204 - 205: 26.987 distance: 205 - 206: 30.108 distance: 205 - 208: 22.820 distance: 206 - 209: 34.770 distance: 209 - 210: 21.729 distance: 210 - 211: 24.025 distance: 210 - 213: 24.366 distance: 211 - 212: 42.930 distance: 211 - 215: 45.993 distance: 213 - 214: 39.504 distance: 216 - 219: 40.052 distance: 217 - 218: 20.932 distance: 217 - 223: 40.477 distance: 219 - 220: 39.438 distance: 220 - 221: 27.450 distance: 220 - 222: 30.654 distance: 223 - 224: 49.061 distance: 223 - 229: 43.762 distance: 224 - 225: 34.706 distance: 224 - 227: 31.186 distance: 225 - 226: 33.924 distance: 225 - 230: 32.460 distance: 227 - 228: 30.762 distance: 228 - 229: 25.059