Starting phenix.real_space_refine on Thu Dec 14 19:54:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/12_2023/8hir_34827_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/12_2023/8hir_34827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/12_2023/8hir_34827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/12_2023/8hir_34827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/12_2023/8hir_34827_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/12_2023/8hir_34827_updated.pdb" } resolution = 3.18 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= 0.007 sd= 0.133 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 K 4 8.98 5 Zn 4 6.06 5 S 208 5.16 5 Na 4 4.78 5 C 18908 2.51 5 N 4848 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C ASP 413": "OD1" <-> "OD2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ASP 504": "OD1" <-> "OD2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 839": "OD1" <-> "OD2" Residue "D TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1014": "OE1" <-> "OE2" Residue "D GLU 1148": "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: 29168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "C" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 17 Unusual residues: {' K': 4, ' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4558 SG CYS A 777 82.687 95.289 12.517 1.00113.91 S ATOM 4564 SG CYS A 778 85.660 98.570 12.340 1.00115.70 S ATOM 4618 SG CYS A 785 86.098 95.282 10.992 1.00138.43 S ATOM 11836 SG CYS B 777 95.308 67.082 12.496 1.00113.48 S ATOM 11842 SG CYS B 778 98.582 64.093 12.329 1.00117.04 S ATOM 11896 SG CYS B 785 95.296 63.676 10.963 1.00136.80 S ATOM 19114 SG CYS C 777 67.051 54.450 12.490 1.00112.86 S ATOM 19120 SG CYS C 778 64.079 51.170 12.324 1.00115.83 S ATOM 19174 SG CYS C 785 63.629 54.465 10.977 1.00137.33 S ATOM 26392 SG CYS D 777 54.468 82.685 12.517 1.00116.50 S ATOM 26398 SG CYS D 778 51.170 85.650 12.341 1.00118.42 S ATOM 26452 SG CYS D 785 54.472 86.094 10.989 1.00137.08 S Time building chain proxies: 15.74, per 1000 atoms: 0.54 Number of scatterers: 29168 At special positions: 0 Unit cell: (150.8, 150.8, 139.36, 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) Zn 4 29.99 K 4 19.00 S 208 16.00 Na 4 11.00 O 5192 8.00 N 4848 7.00 C 18908 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: 11.05 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1307 " pdb="ZN ZN A1307 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 778 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 777 " pdb=" ZN C1303 " pdb="ZN ZN C1303 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 778 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 777 " pdb=" ZN D1303 " pdb="ZN ZN D1303 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 778 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 777 " Number of angles added : 12 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 24 sheets defined 44.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.52 Creating SS restraints... Processing helix chain 'A' and resid 91 through 94 No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 109 through 135 removed outlier: 3.790A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 175 through 197 Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.600A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 4.857A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.533A pdb=" N GLU A 250 " --> pdb=" O HIS A 247 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 294 removed outlier: 4.118A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 325 through 357 Proline residue: A 343 - end of helix removed outlier: 4.242A pdb=" N GLU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.516A pdb=" N ASN A 391 " --> pdb=" O MET A 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.136A pdb=" N ARG A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.870A pdb=" N ARG A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 removed outlier: 4.010A pdb=" N THR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.590A pdb=" N ALA A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.601A pdb=" N THR A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.540A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 776 through 779 No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 793 through 796 No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.614A pdb=" N ASN A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Proline residue: A 820 - end of helix No H-bonds generated for 'chain 'A' and resid 812 through 822' Processing helix chain 'A' and resid 844 through 850 removed outlier: 3.837A pdb=" N ALA A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 894 through 897 No H-bonds generated for 'chain 'A' and resid 894 through 897' Processing helix chain 'A' and resid 899 through 911 removed outlier: 3.657A pdb=" N VAL A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 929 removed outlier: 4.100A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 removed outlier: 3.512A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 965 No H-bonds generated for 'chain 'A' and resid 962 through 965' Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.589A pdb=" N TYR A 980 " --> pdb=" O THR A 977 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 981 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1022 through 1032 Processing helix chain 'A' and resid 1133 through 1140 removed outlier: 3.625A pdb=" N LEU A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1160 Processing helix chain 'B' and resid 91 through 94 No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.541A pdb=" N LEU B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 135 removed outlier: 3.767A pdb=" N LEU B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 175 through 197 Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.616A pdb=" N GLU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix removed outlier: 4.701A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.552A pdb=" N GLU B 250 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 294 removed outlier: 4.040A pdb=" N ILE B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 325 through 357 Proline residue: B 343 - end of helix removed outlier: 4.236A pdb=" N GLU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 357 " --> pdb=" O TRP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.501A pdb=" N ASN B 391 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 414 through 419 removed outlier: 4.121A pdb=" N ARG B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 419' Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.896A pdb=" N ARG B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 481 removed outlier: 3.999A pdb=" N THR B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 497 Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.591A pdb=" N ALA B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.601A pdb=" N THR B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 removed outlier: 3.529A pdb=" N GLY B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 776 through 779 No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 793 through 796 No H-bonds generated for 'chain 'B' and resid 793 through 796' Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.635A pdb=" N ASN B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 817 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix No H-bonds generated for 'chain 'B' and resid 812 through 822' Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.830A pdb=" N ALA B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 872 Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 894 through 897 No H-bonds generated for 'chain 'B' and resid 894 through 897' Processing helix chain 'B' and resid 899 through 911 removed outlier: 3.659A pdb=" N VAL B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 4.112A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 removed outlier: 3.504A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 972 through 974 No H-bonds generated for 'chain 'B' and resid 972 through 974' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.566A pdb=" N TYR B 980 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 981 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 995 Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1022 through 1032 Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 3.624A pdb=" N LEU B1138 " --> pdb=" O SER B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1160 Processing helix chain 'C' and resid 91 through 94 No H-bonds generated for 'chain 'C' and resid 91 through 94' Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 109 through 135 removed outlier: 3.783A pdb=" N LEU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 175 through 197 Processing helix chain 'C' and resid 205 through 208 No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.620A pdb=" N GLU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Proline residue: C 221 - end of helix removed outlier: 4.887A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 255 removed outlier: 3.556A pdb=" N GLU C 250 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 254 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 294 removed outlier: 3.981A pdb=" N ILE C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 325 through 357 Proline residue: C 343 - end of helix removed outlier: 4.240A pdb=" N GLU C 355 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 357 " --> pdb=" O TRP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 368 No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 383 through 393 removed outlier: 3.591A pdb=" N ASN C 391 " --> pdb=" O MET C 387 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 414 through 420 removed outlier: 4.104A pdb=" N ARG C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.888A pdb=" N ARG C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 481 removed outlier: 4.004A pdb=" N THR C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.591A pdb=" N ALA C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 533 removed outlier: 3.618A pdb=" N THR C 531 " --> pdb=" O SER C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 558 removed outlier: 3.535A pdb=" N GLY C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 590 Processing helix chain 'C' and resid 630 through 632 No H-bonds generated for 'chain 'C' and resid 630 through 632' Processing helix chain 'C' and resid 776 through 779 No H-bonds generated for 'chain 'C' and resid 776 through 779' Processing helix chain 'C' and resid 793 through 796 No H-bonds generated for 'chain 'C' and resid 793 through 796' Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.636A pdb=" N ASN C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 817 " --> pdb=" O GLY C 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Proline residue: C 820 - end of helix No H-bonds generated for 'chain 'C' and resid 812 through 822' Processing helix chain 'C' and resid 844 through 850 removed outlier: 3.832A pdb=" N ALA C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 872 Processing helix chain 'C' and resid 874 through 876 No H-bonds generated for 'chain 'C' and resid 874 through 876' Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 894 through 897 No H-bonds generated for 'chain 'C' and resid 894 through 897' Processing helix chain 'C' and resid 899 through 911 removed outlier: 3.664A pdb=" N VAL C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 910 " --> pdb=" O GLN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 929 removed outlier: 4.094A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 952 removed outlier: 3.513A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 965 No H-bonds generated for 'chain 'C' and resid 962 through 965' Processing helix chain 'C' and resid 972 through 974 No H-bonds generated for 'chain 'C' and resid 972 through 974' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.566A pdb=" N TYR C 980 " --> pdb=" O THR C 977 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 981 " --> pdb=" O LEU C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 995 Processing helix chain 'C' and resid 1014 through 1016 No H-bonds generated for 'chain 'C' and resid 1014 through 1016' Processing helix chain 'C' and resid 1022 through 1032 Processing helix chain 'C' and resid 1133 through 1140 removed outlier: 3.619A pdb=" N LEU C1138 " --> pdb=" O SER C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1160 Processing helix chain 'D' and resid 91 through 94 No H-bonds generated for 'chain 'D' and resid 91 through 94' Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.517A pdb=" N LEU D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 135 removed outlier: 3.760A pdb=" N LEU D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 165 through 168 No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 175 through 197 Processing helix chain 'D' and resid 205 through 208 No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 210 through 226 removed outlier: 3.598A pdb=" N GLU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.845A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.643A pdb=" N GLU D 250 " --> pdb=" O HIS D 247 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 294 removed outlier: 4.119A pdb=" N ILE D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 325 through 357 Proline residue: D 343 - end of helix removed outlier: 4.240A pdb=" N GLU D 355 " --> pdb=" O TYR D 351 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN D 357 " --> pdb=" O TRP D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 368 No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 383 through 393 removed outlier: 3.520A pdb=" N ASN D 391 " --> pdb=" O MET D 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 414 through 420 removed outlier: 4.133A pdb=" N ARG D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.876A pdb=" N ARG D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 481 removed outlier: 4.008A pdb=" N THR D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.589A pdb=" N ALA D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 533 removed outlier: 3.602A pdb=" N THR D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.567A pdb=" N GLY D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY D 558 " --> pdb=" O GLY D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 630 through 632 No H-bonds generated for 'chain 'D' and resid 630 through 632' Processing helix chain 'D' and resid 776 through 779 No H-bonds generated for 'chain 'D' and resid 776 through 779' Processing helix chain 'D' and resid 793 through 796 No H-bonds generated for 'chain 'D' and resid 793 through 796' Processing helix chain 'D' and resid 812 through 822 removed outlier: 3.612A pdb=" N ASN D 816 " --> pdb=" O ASN D 812 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 817 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Proline residue: D 820 - end of helix No H-bonds generated for 'chain 'D' and resid 812 through 822' Processing helix chain 'D' and resid 844 through 850 removed outlier: 3.838A pdb=" N ALA D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 872 Processing helix chain 'D' and resid 874 through 876 No H-bonds generated for 'chain 'D' and resid 874 through 876' Processing helix chain 'D' and resid 888 through 890 No H-bonds generated for 'chain 'D' and resid 888 through 890' Processing helix chain 'D' and resid 894 through 897 No H-bonds generated for 'chain 'D' and resid 894 through 897' Processing helix chain 'D' and resid 899 through 911 removed outlier: 3.686A pdb=" N VAL D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 910 " --> pdb=" O GLN D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 929 removed outlier: 4.108A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 952 removed outlier: 3.502A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 946 " --> pdb=" O LEU D 942 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 965 No H-bonds generated for 'chain 'D' and resid 962 through 965' Processing helix chain 'D' and resid 972 through 974 No H-bonds generated for 'chain 'D' and resid 972 through 974' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.586A pdb=" N TYR D 980 " --> pdb=" O THR D 977 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN D 981 " --> pdb=" O LEU D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 995 Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1022 through 1032 Processing helix chain 'D' and resid 1133 through 1140 removed outlier: 3.617A pdb=" N LEU D1138 " --> pdb=" O SER D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1160 Processing sheet with id= A, first strand: chain 'A' and resid 505 through 508 removed outlier: 6.129A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LEU A 456 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N CYS A 377 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 408 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.832A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 750 through 753 Processing sheet with id= D, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.297A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE A 804 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 880 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 916 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 882 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 918 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.094A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1039 through 1044 Processing sheet with id= G, first strand: chain 'B' and resid 505 through 508 removed outlier: 6.132A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LEU B 456 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N CYS B 377 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 408 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.866A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 750 through 753 Processing sheet with id= J, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.275A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE B 804 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 880 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER B 916 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL B 882 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 918 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 4.129A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1039 through 1044 Processing sheet with id= M, first strand: chain 'C' and resid 505 through 508 removed outlier: 6.151A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU C 456 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N CYS C 377 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 408 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.861A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 750 through 753 Processing sheet with id= P, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.271A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE C 804 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 880 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 916 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 882 " --> pdb=" O SER C 916 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C 918 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 4.112A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1039 through 1044 Processing sheet with id= S, first strand: chain 'D' and resid 505 through 508 removed outlier: 6.136A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU D 456 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS D 377 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS D 408 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.840A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 750 through 753 Processing sheet with id= V, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.291A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE D 804 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU D 880 " --> pdb=" O ILE D 804 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 916 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL D 882 " --> pdb=" O SER D 916 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 918 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 4.104A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1039 through 1044 983 hydrogen bonds defined for protein. 2667 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: 9.92 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9201 1.34 - 1.46: 6777 1.46 - 1.58: 13562 1.58 - 1.70: 0 1.70 - 1.81: 304 Bond restraints: 29844 Sorted by residual: bond pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 1.492 1.390 0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" CA PRO C 229 " pdb=" C PRO C 229 " ideal model delta sigma weight residual 1.517 1.536 -0.019 9.30e-03 1.16e+04 4.13e+00 bond pdb=" CA ILE C 203 " pdb=" CB ILE C 203 " ideal model delta sigma weight residual 1.540 1.563 -0.023 1.36e-02 5.41e+03 2.88e+00 bond pdb=" CA ILE B 203 " pdb=" CB ILE B 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 bond pdb=" CA ILE D 203 " pdb=" CB ILE D 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 ... (remaining 29839 not shown) Histogram of bond angle deviations from ideal: 82.95 - 93.59: 8 93.59 - 104.23: 457 104.23 - 114.87: 18106 114.87 - 125.51: 21448 125.51 - 136.15: 481 Bond angle restraints: 40500 Sorted by residual: angle pdb=" N ARG D 172 " pdb=" CA ARG D 172 " pdb=" C ARG D 172 " ideal model delta sigma weight residual 109.79 82.95 26.84 1.56e+00 4.11e-01 2.96e+02 angle pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" C ARG A 172 " ideal model delta sigma weight residual 109.79 83.15 26.64 1.56e+00 4.11e-01 2.92e+02 angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.79 83.30 26.49 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.79 83.31 26.48 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N LYS C 173 " pdb=" CA LYS C 173 " pdb=" CB LYS C 173 " ideal model delta sigma weight residual 110.39 91.56 18.83 1.59e+00 3.96e-01 1.40e+02 ... (remaining 40495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15553 17.94 - 35.89: 1825 35.89 - 53.83: 393 53.83 - 71.77: 65 71.77 - 89.71: 16 Dihedral angle restraints: 17852 sinusoidal: 7008 harmonic: 10844 Sorted by residual: dihedral pdb=" C ARG A 172 " pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" CB ARG A 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG B 172 " pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" CB ARG B 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG C 172 " pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" CB ARG C 172 " ideal model delta harmonic sigma weight residual -122.60 -106.87 -15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 17849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 4522 0.115 - 0.229: 73 0.229 - 0.344: 5 0.344 - 0.458: 6 0.458 - 0.573: 6 Chirality restraints: 4612 Sorted by residual: chirality pdb=" CA ILE B 203 " pdb=" N ILE B 203 " pdb=" C ILE B 203 " pdb=" CB ILE B 203 " both_signs ideal model delta sigma weight residual False 2.43 3.01 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA ARG B 172 " pdb=" N ARG B 172 " pdb=" C ARG B 172 " pdb=" CB ARG B 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 4609 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 228 " 0.076 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 229 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 229 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 229 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B1191 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B1192 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B1192 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1192 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1191 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C1192 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C1192 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1192 " -0.029 5.00e-02 4.00e+02 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 389 2.63 - 3.26: 30260 3.26 - 3.88: 56163 3.88 - 4.51: 77858 4.51 - 5.14: 123749 Nonbonded interactions: 288419 Sorted by model distance: nonbonded pdb=" N ARG D 172 " pdb=" O ARG D 172 " model vdw 2.000 2.496 nonbonded pdb=" N ARG A 172 " pdb=" O ARG A 172 " model vdw 2.005 2.496 nonbonded pdb=" N ARG C 172 " pdb=" O ARG C 172 " model vdw 2.006 2.496 nonbonded pdb=" N ARG B 172 " pdb=" O ARG B 172 " model vdw 2.008 2.496 nonbonded pdb=" OD2 ASP C 468 " pdb=" ND2 ASN C 496 " model vdw 2.055 2.520 ... (remaining 288414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 85 through 1205) selection = (chain 'B' and resid 85 through 1205) selection = (chain 'C' and resid 85 through 1205) selection = (chain 'D' and resid 85 through 1205) } 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: 1.220 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: 0.020 Extract box with map and model: 5.560 Check model and map are aligned: 0.440 Set scattering table: 0.240 Process input model: 80.340 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.150 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.003 0.102 29844 Z= 0.187 Angle : 0.768 26.841 40500 Z= 0.427 Chirality : 0.049 0.573 4612 Planarity : 0.004 0.106 5088 Dihedral : 15.768 89.714 10828 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 22.31 % Favored : 77.59 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.13), residues: 3632 helix: -1.67 (0.12), residues: 1636 sheet: -1.42 (0.26), residues: 396 loop : -0.45 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 177 HIS 0.004 0.001 HIS C 586 PHE 0.025 0.001 PHE D 932 TYR 0.025 0.001 TYR A 130 ARG 0.009 0.001 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 560 time to evaluate : 3.419 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 561 average time/residue: 0.4554 time to fit residues: 394.0344 Evaluate side-chains 515 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 514 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2512 time to fit residues: 5.0574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 285 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 330 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 119 ASN A 151 GLN A 241 ASN A 291 HIS A 369 GLN A 490 GLN A 499 HIS A 505 HIS A 844 HIS A 871 GLN A 879 ASN A 923 HIS A 955 ASN A1147 GLN B 108 ASN B 119 ASN B 151 GLN B 241 ASN B 291 HIS B 369 GLN B 490 GLN B 499 HIS B 505 HIS B 844 HIS B 871 GLN B 879 ASN B 955 ASN B1147 GLN C 108 ASN C 119 ASN C 151 GLN C 241 ASN C 369 GLN C 490 GLN C 499 HIS C 505 HIS C 844 HIS C 871 GLN C 879 ASN C 955 ASN C1147 GLN D 108 ASN D 119 ASN D 151 GLN D 241 ASN D 291 HIS D 369 GLN D 490 GLN D 499 HIS D 505 HIS D 844 HIS D 871 GLN D 879 ASN D 955 ASN D1147 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 29844 Z= 0.399 Angle : 0.648 13.012 40500 Z= 0.326 Chirality : 0.046 0.243 4612 Planarity : 0.004 0.042 5088 Dihedral : 4.834 40.204 4020 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.39 % Allowed : 22.41 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.14), residues: 3632 helix: -1.00 (0.12), residues: 1628 sheet: -1.39 (0.25), residues: 416 loop : -0.45 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 177 HIS 0.005 0.001 HIS C 586 PHE 0.028 0.002 PHE D 932 TYR 0.017 0.002 TYR A 130 ARG 0.004 0.000 ARG D 828 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 553 time to evaluate : 3.537 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 67 residues processed: 631 average time/residue: 0.4406 time to fit residues: 433.2885 Evaluate side-chains 580 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 513 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.2936 time to fit residues: 40.3768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 275 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 331 optimal weight: 0.4980 chunk 357 optimal weight: 9.9990 chunk 294 optimal weight: 0.9990 chunk 328 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 923 HIS C 108 ASN D 400 GLN D 923 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29844 Z= 0.168 Angle : 0.554 13.496 40500 Z= 0.275 Chirality : 0.042 0.205 4612 Planarity : 0.004 0.045 5088 Dihedral : 4.501 35.933 4020 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.84 % Allowed : 22.15 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.14), residues: 3632 helix: -0.63 (0.13), residues: 1640 sheet: -1.11 (0.26), residues: 404 loop : -0.35 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 177 HIS 0.005 0.001 HIS D 586 PHE 0.032 0.001 PHE C 97 TYR 0.013 0.001 TYR A 130 ARG 0.004 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 590 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 20 residues processed: 631 average time/residue: 0.4373 time to fit residues: 429.5008 Evaluate side-chains 536 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 516 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2794 time to fit residues: 14.8853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 332 optimal weight: 0.0050 chunk 351 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 HIS C 108 ASN D 844 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29844 Z= 0.240 Angle : 0.576 13.948 40500 Z= 0.283 Chirality : 0.043 0.214 4612 Planarity : 0.004 0.046 5088 Dihedral : 4.452 35.411 4020 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.12 % Allowed : 23.04 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.14), residues: 3632 helix: -0.51 (0.13), residues: 1640 sheet: -1.15 (0.25), residues: 412 loop : -0.36 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 353 HIS 0.005 0.001 HIS D 586 PHE 0.029 0.001 PHE C 97 TYR 0.016 0.001 TYR B 876 ARG 0.003 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 550 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 40 residues processed: 588 average time/residue: 0.4349 time to fit residues: 397.0182 Evaluate side-chains 546 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 506 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2750 time to fit residues: 24.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 5 optimal weight: 0.0070 chunk 261 optimal weight: 0.0770 chunk 145 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 179 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 overall best weight: 1.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1046 HIS C 108 ASN C 923 HIS D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29844 Z= 0.188 Angle : 0.560 14.642 40500 Z= 0.274 Chirality : 0.042 0.233 4612 Planarity : 0.004 0.051 5088 Dihedral : 4.343 32.722 4020 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.27 % Allowed : 23.67 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.14), residues: 3632 helix: -0.34 (0.13), residues: 1644 sheet: -1.12 (0.25), residues: 412 loop : -0.24 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.005 0.001 HIS D 586 PHE 0.031 0.001 PHE C 97 TYR 0.015 0.001 TYR D1167 ARG 0.007 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 545 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 11 residues processed: 572 average time/residue: 0.4591 time to fit residues: 410.0488 Evaluate side-chains 522 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 511 time to evaluate : 3.262 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2759 time to fit residues: 10.0110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.0670 chunk 316 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 586 HIS C 586 HIS C1046 HIS D 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29844 Z= 0.162 Angle : 0.562 14.926 40500 Z= 0.274 Chirality : 0.042 0.244 4612 Planarity : 0.003 0.052 5088 Dihedral : 4.205 29.343 4020 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.89 % Allowed : 23.96 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.14), residues: 3632 helix: -0.17 (0.13), residues: 1644 sheet: -1.02 (0.26), residues: 404 loop : -0.18 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.005 0.001 HIS D 586 PHE 0.026 0.001 PHE C 97 TYR 0.024 0.001 TYR B 582 ARG 0.006 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 557 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 574 average time/residue: 0.4453 time to fit residues: 397.3208 Evaluate side-chains 526 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 517 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2759 time to fit residues: 8.9312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 196 optimal weight: 30.0000 chunk 350 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 586 HIS A1046 HIS B 108 ASN D 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29844 Z= 0.195 Angle : 0.578 14.431 40500 Z= 0.280 Chirality : 0.043 0.251 4612 Planarity : 0.004 0.050 5088 Dihedral : 4.199 28.628 4020 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.79 % Allowed : 24.49 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.14), residues: 3632 helix: -0.12 (0.13), residues: 1644 sheet: -1.02 (0.26), residues: 404 loop : -0.14 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.006 0.001 HIS A 586 PHE 0.026 0.001 PHE C 97 TYR 0.020 0.001 TYR B 876 ARG 0.007 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 535 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 552 average time/residue: 0.4467 time to fit residues: 381.7914 Evaluate side-chains 525 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 517 time to evaluate : 3.293 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2595 time to fit residues: 8.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 239 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 206 GLN D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29844 Z= 0.175 Angle : 0.578 15.525 40500 Z= 0.279 Chirality : 0.042 0.256 4612 Planarity : 0.003 0.051 5088 Dihedral : 4.134 26.496 4020 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.47 % Allowed : 24.84 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.14), residues: 3632 helix: -0.01 (0.13), residues: 1624 sheet: -0.98 (0.26), residues: 404 loop : -0.10 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 353 HIS 0.005 0.000 HIS D 586 PHE 0.029 0.001 PHE C 97 TYR 0.023 0.001 TYR A 582 ARG 0.007 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 534 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 540 average time/residue: 0.4568 time to fit residues: 380.2540 Evaluate side-chains 523 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 519 time to evaluate : 3.425 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2804 time to fit residues: 6.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 65.1121 > 50: distance: 58 - 79: 15.440 distance: 62 - 87: 22.713 distance: 74 - 79: 18.646 distance: 79 - 80: 25.275 distance: 80 - 81: 20.616 distance: 80 - 83: 27.027 distance: 81 - 82: 23.488 distance: 81 - 87: 3.851 distance: 83 - 84: 9.280 distance: 83 - 85: 16.536 distance: 84 - 86: 10.988 distance: 87 - 88: 13.346 distance: 88 - 89: 28.608 distance: 88 - 91: 9.956 distance: 89 - 90: 39.015 distance: 89 - 94: 18.649 distance: 91 - 92: 19.917 distance: 91 - 93: 14.251 distance: 94 - 95: 27.842 distance: 95 - 96: 10.310 distance: 95 - 98: 32.540 distance: 96 - 97: 30.543 distance: 96 - 102: 43.728 distance: 98 - 99: 10.095 distance: 98 - 100: 32.366 distance: 99 - 101: 34.018 distance: 102 - 103: 5.985 distance: 103 - 104: 35.190 distance: 103 - 106: 12.810 distance: 104 - 105: 16.621 distance: 104 - 113: 42.674 distance: 106 - 107: 19.332 distance: 107 - 108: 19.030 distance: 107 - 109: 21.145 distance: 108 - 110: 6.178 distance: 109 - 111: 7.874 distance: 110 - 112: 8.468 distance: 113 - 114: 9.312 distance: 114 - 115: 11.909 distance: 114 - 117: 43.301 distance: 115 - 116: 29.771 distance: 115 - 127: 31.582 distance: 118 - 119: 28.625 distance: 118 - 120: 18.781 distance: 119 - 121: 26.034 distance: 120 - 122: 10.359 distance: 120 - 123: 3.251 distance: 121 - 122: 5.558 distance: 122 - 124: 6.555 distance: 123 - 125: 11.794 distance: 124 - 126: 6.950 distance: 125 - 126: 7.394 distance: 127 - 128: 34.193 distance: 127 - 133: 16.232 distance: 128 - 129: 36.816 distance: 128 - 131: 36.105 distance: 129 - 130: 27.121 distance: 129 - 134: 31.609 distance: 131 - 132: 10.597 distance: 132 - 133: 44.051 distance: 134 - 135: 24.068 distance: 134 - 140: 20.187 distance: 135 - 136: 17.000 distance: 135 - 138: 35.675 distance: 136 - 137: 16.523 distance: 136 - 141: 8.210 distance: 138 - 139: 10.254 distance: 139 - 140: 38.001 distance: 141 - 142: 11.321 distance: 142 - 143: 14.682 distance: 142 - 145: 27.601 distance: 143 - 144: 19.246 distance: 143 - 149: 20.261 distance: 145 - 146: 12.202 distance: 146 - 147: 31.689 distance: 146 - 148: 34.982 distance: 149 - 150: 11.195 distance: 150 - 151: 40.310 distance: 150 - 153: 42.348 distance: 151 - 152: 14.317 distance: 151 - 160: 21.904 distance: 153 - 154: 34.439 distance: 154 - 155: 21.347 distance: 155 - 156: 12.662 distance: 156 - 157: 17.871 distance: 157 - 158: 15.690 distance: 157 - 159: 5.813 distance: 160 - 161: 50.777 distance: 161 - 162: 15.604 distance: 161 - 164: 27.104 distance: 162 - 163: 42.808 distance: 162 - 165: 28.828