Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 21:08:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/08_2023/7rza_24756_updated.pdb" } resolution = 4.26 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 17894 2.51 5 N 4618 2.21 5 O 5194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1089": "NH1" <-> "NH2" Residue "A ARG 1111": "NH1" <-> "NH2" Residue "A PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 715": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 715": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1089": "NH1" <-> "NH2" Residue "C ARG 1111": "NH1" <-> "NH2" Residue "C PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 715": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 27850 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7713 Classifications: {'peptide': 981} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 952} Chain breaks: 3 Chain: "B" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6186 Classifications: {'peptide': 785} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 761} Chain breaks: 2 Chain: "C" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7713 Classifications: {'peptide': 981} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 952} Chain breaks: 3 Chain: "D" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6186 Classifications: {'peptide': 785} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 761} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.60, per 1000 atoms: 0.45 Number of scatterers: 27850 At special positions: 0 Unit cell: (122.01, 163.51, 185.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5194 8.00 N 4618 7.00 C 17894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.04 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 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: 9.79 Conformation dependent library (CDL) restraints added in 3.6 seconds 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 38 sheets defined 43.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.607A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.644A pdb=" N THR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.523A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.698A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.581A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.605A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.682A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.744A pdb=" N GLU A 330 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 334 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.545A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 523 through 546 removed outlier: 3.782A pdb=" N ARG A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.828A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 626 removed outlier: 3.624A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.537A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.588A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 756 removed outlier: 3.540A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.577A pdb=" N VAL A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 751 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 753 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 756 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.634A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) 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 821 Processing helix chain 'A' and resid 1005 through 1028 removed outlier: 3.896A pdb=" N ALA A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1011 " --> pdb=" O GLY A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1147 removed outlier: 3.725A pdb=" N LEU A1127 " --> pdb=" O GLY A1123 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A1130 " --> pdb=" O TRP A1126 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A1145 " --> pdb=" O VAL A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1193 removed outlier: 3.572A pdb=" N ALA A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1167 " --> pdb=" O ASN A1163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A1185 " --> pdb=" O HIS A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1232 removed outlier: 3.745A pdb=" N MET A1221 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1222 " --> pdb=" O THR A1218 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A1223 " --> pdb=" O CYS A1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.707A pdb=" N ARG B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.801A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.522A pdb=" N LEU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.705A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 Processing helix chain 'B' and resid 198 through 211 removed outlier: 4.039A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.625A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.539A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.652A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.586A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.547A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) Proline residue: B 520 - end of helix No H-bonds generated for 'chain 'B' and resid 516 through 520' Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.682A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.914A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 3.706A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.740A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 675 " --> pdb=" O TRP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.988A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 712 " --> pdb=" O MET B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 4.184A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 3.576A pdb=" N LYS B 752 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 753 " --> pdb=" O VAL B 750 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 755 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.758A pdb=" N LYS B 765 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 793 through 819 removed outlier: 3.680A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 removed outlier: 3.606A pdb=" N GLY C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.645A pdb=" N THR C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.523A pdb=" N ILE C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.698A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.581A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.605A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.682A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.743A pdb=" N GLU C 330 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 334 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 469 removed outlier: 3.545A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 523 through 546 removed outlier: 3.782A pdb=" N ARG C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.827A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 626 removed outlier: 3.624A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.536A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.589A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 756 removed outlier: 3.540A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 3.577A pdb=" N VAL C 750 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 751 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 753 " --> pdb=" O VAL C 750 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 756 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.634A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) 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 821 Processing helix chain 'C' and resid 1005 through 1028 removed outlier: 3.896A pdb=" N ALA C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C1011 " --> pdb=" O GLY C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1147 removed outlier: 3.723A pdb=" N LEU C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C1130 " --> pdb=" O TRP C1126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C1145 " --> pdb=" O VAL C1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1193 removed outlier: 3.573A pdb=" N ALA C1166 " --> pdb=" O LEU C1162 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C1167 " --> pdb=" O ASN C1163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C1185 " --> pdb=" O HIS C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1232 removed outlier: 3.746A pdb=" N MET C1221 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C1222 " --> pdb=" O THR C1218 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C1223 " --> pdb=" O CYS C1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.706A pdb=" N ARG D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.800A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.524A pdb=" N LEU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 156 removed outlier: 3.706A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 Processing helix chain 'D' and resid 198 through 211 removed outlier: 4.039A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.626A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.538A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.501A pdb=" N ARG D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 435 removed outlier: 3.652A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 removed outlier: 3.587A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.547A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) Proline residue: D 520 - end of helix No H-bonds generated for 'chain 'D' and resid 516 through 520' Processing helix chain 'D' and resid 523 through 546 removed outlier: 3.682A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.914A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.706A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 676 removed outlier: 3.740A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 675 " --> pdb=" O TRP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 694 Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.987A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 755 removed outlier: 4.183A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 3.576A pdb=" N LYS D 752 " --> pdb=" O ALA D 749 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 753 " --> pdb=" O VAL D 750 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 755 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 769 removed outlier: 3.757A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 780 Processing helix chain 'D' and resid 793 through 819 removed outlier: 3.679A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 50 removed outlier: 3.573A pdb=" N ILE A 12 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER A 95 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY A 75 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 97 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 161 through 164 removed outlier: 3.678A pdb=" N TYR A 137 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 193 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.414A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= E, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.665A pdb=" N VAL A 381 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'A' and resid 489 through 491 removed outlier: 3.555A pdb=" N THR A 736 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.973A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.925A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1033 through 1039 removed outlier: 3.508A pdb=" N THR A1093 " --> pdb=" O CYS A1033 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1097 through 1100 Processing sheet with id= L, first strand: chain 'B' and resid 11 through 13 removed outlier: 7.486A pdb=" N ARG B 42 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 47 through 50 removed outlier: 7.445A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 72 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LEU B 17 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 75 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.202A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 361 through 364 removed outlier: 3.526A pdb=" N ARG B 369 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= Q, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= R, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.657A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 730 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.512A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 42 through 50 removed outlier: 3.572A pdb=" N ILE C 12 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER C 95 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLY C 75 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 97 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.678A pdb=" N TYR C 137 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 193 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.414A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= X, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.666A pdb=" N VAL C 381 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= Z, first strand: chain 'C' and resid 489 through 491 removed outlier: 3.555A pdb=" N THR C 736 " --> pdb=" O ASP C 490 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.974A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.925A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 1033 through 1039 removed outlier: 3.508A pdb=" N THR C1093 " --> pdb=" O CYS C1033 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 1097 through 1100 Processing sheet with id= AE, first strand: chain 'D' and resid 11 through 13 removed outlier: 7.487A pdb=" N ARG D 42 " --> pdb=" O ILE D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'D' and resid 47 through 50 removed outlier: 7.444A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA D 72 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LEU D 17 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 75 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.201A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 361 through 364 removed outlier: 3.526A pdb=" N ARG D 369 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AJ, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AK, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.656A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 730 " --> pdb=" O LEU D 498 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.512A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2937 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: 8.63 Time building geometry restraints manager: 10.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8830 1.35 - 1.47: 7253 1.47 - 1.60: 12135 1.60 - 1.72: 4 1.72 - 1.85: 230 Bond restraints: 28452 Sorted by residual: bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.185 1.449 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.185 1.448 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C05 QUS A1401 " pdb=" O19 QUS A1401 " ideal model delta sigma weight residual 1.185 1.448 -0.263 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C05 QUS C1401 " pdb=" O19 QUS C1401 " ideal model delta sigma weight residual 1.185 1.447 -0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C04 QUS D1301 " pdb=" O18 QUS D1301 " ideal model delta sigma weight residual 1.185 1.412 -0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 28447 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.90: 478 105.90 - 112.99: 15133 112.99 - 120.07: 9929 120.07 - 127.16: 12651 127.16 - 134.25: 275 Bond angle restraints: 38466 Sorted by residual: angle pdb=" C SER C1153 " pdb=" N SER C1154 " pdb=" CA SER C1154 " ideal model delta sigma weight residual 120.79 128.78 -7.99 1.39e+00 5.18e-01 3.31e+01 angle pdb=" C SER A1153 " pdb=" N SER A1154 " pdb=" CA SER A1154 " ideal model delta sigma weight residual 120.79 128.73 -7.94 1.39e+00 5.18e-01 3.26e+01 angle pdb=" N LEU B 233 " pdb=" CA LEU B 233 " pdb=" C LEU B 233 " ideal model delta sigma weight residual 113.72 106.55 7.17 1.30e+00 5.92e-01 3.04e+01 angle pdb=" N LEU D 233 " pdb=" CA LEU D 233 " pdb=" C LEU D 233 " ideal model delta sigma weight residual 113.72 106.57 7.15 1.30e+00 5.92e-01 3.02e+01 angle pdb=" C GLY D 774 " pdb=" N ALA D 775 " pdb=" CA ALA D 775 " ideal model delta sigma weight residual 120.38 128.40 -8.02 1.46e+00 4.69e-01 3.02e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 15612 14.98 - 29.95: 865 29.95 - 44.93: 293 44.93 - 59.90: 42 59.90 - 74.88: 14 Dihedral angle restraints: 16826 sinusoidal: 6664 harmonic: 10162 Sorted by residual: dihedral pdb=" CA ASN B 318 " pdb=" C ASN B 318 " pdb=" N PRO B 319 " pdb=" CA PRO B 319 " ideal model delta harmonic sigma weight residual -180.00 -119.12 -60.88 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ASN D 318 " pdb=" C ASN D 318 " pdb=" N PRO D 319 " pdb=" CA PRO D 319 " ideal model delta harmonic sigma weight residual -180.00 -119.12 -60.88 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ASN C 318 " pdb=" C ASN C 318 " pdb=" N PRO C 319 " pdb=" CA PRO C 319 " ideal model delta harmonic sigma weight residual 180.00 -131.75 -48.25 0 5.00e+00 4.00e-02 9.31e+01 ... (remaining 16823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3213 0.054 - 0.109: 865 0.109 - 0.163: 168 0.163 - 0.218: 22 0.218 - 0.272: 6 Chirality restraints: 4274 Sorted by residual: chirality pdb=" CB VAL B 165 " pdb=" CA VAL B 165 " pdb=" CG1 VAL B 165 " pdb=" CG2 VAL B 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL D 165 " pdb=" CA VAL D 165 " pdb=" CG1 VAL D 165 " pdb=" CG2 VAL D 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 4271 not shown) Planarity restraints: 4846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO B 99 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO D 99 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO C 99 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.040 5.00e-02 4.00e+02 ... (remaining 4843 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6582 2.78 - 3.31: 25506 3.31 - 3.84: 45056 3.84 - 4.37: 53034 4.37 - 4.90: 88660 Nonbonded interactions: 218838 Sorted by model distance: nonbonded pdb=" OG SER B 729 " pdb=" OG SER C 729 " model vdw 2.247 2.440 nonbonded pdb=" O VAL A 681 " pdb=" OH TYR A 700 " model vdw 2.248 2.440 nonbonded pdb=" O VAL C 681 " pdb=" OH TYR C 700 " model vdw 2.248 2.440 nonbonded pdb=" OG1 THR C 655 " pdb=" O18 QUS C1401 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 655 " pdb=" O18 QUS A1401 " model vdw 2.263 2.440 ... (remaining 218833 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 11.850 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 63.550 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.170 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.007 0.264 28452 Z= 0.480 Angle : 0.976 13.071 38466 Z= 0.564 Chirality : 0.052 0.272 4274 Planarity : 0.006 0.076 4846 Dihedral : 11.116 74.876 10304 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.18 % 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: -4.39 (0.11), residues: 3504 helix: -3.41 (0.07), residues: 1648 sheet: -2.54 (0.22), residues: 432 loop : -2.11 (0.14), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 849 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 859 average time/residue: 0.4168 time to fit residues: 554.5550 Evaluate side-chains 468 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 466 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2440 time to fit residues: 5.5955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 chunk 148 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 275 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 chunk 319 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 HIS A1152 HIS A1202 HIS B 46 HIS B 207 GLN B 246 GLN B 274 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN C 246 GLN ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 HIS C1202 HIS D 46 HIS D 207 GLN D 246 GLN D 274 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28452 Z= 0.190 Angle : 0.579 9.874 38466 Z= 0.309 Chirality : 0.042 0.279 4274 Planarity : 0.005 0.081 4846 Dihedral : 5.562 52.491 3826 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -2.33 (0.12), residues: 3504 helix: -1.16 (0.11), residues: 1632 sheet: -2.38 (0.21), residues: 442 loop : -1.52 (0.15), residues: 1430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 614 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 616 average time/residue: 0.3644 time to fit residues: 364.5448 Evaluate side-chains 426 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 3.071 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 2.9990 chunk 99 optimal weight: 0.0060 chunk 266 optimal weight: 0.0980 chunk 217 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 320 optimal weight: 0.9990 chunk 345 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 317 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 46 HIS B 107 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS D 24 GLN D 83 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 28452 Z= 0.144 Angle : 0.509 7.253 38466 Z= 0.267 Chirality : 0.040 0.200 4274 Planarity : 0.004 0.065 4846 Dihedral : 4.871 49.716 3826 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3504 helix: 0.04 (0.12), residues: 1636 sheet: -2.31 (0.22), residues: 442 loop : -1.35 (0.15), residues: 1426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 580 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 581 average time/residue: 0.3667 time to fit residues: 348.6105 Evaluate side-chains 406 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 340 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 304 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS A 412 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 214 HIS B 298 ASN B 359 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 219 HIS ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 107 HIS D 207 GLN D 214 HIS D 298 ASN D 359 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 28452 Z= 0.301 Angle : 0.642 9.510 38466 Z= 0.336 Chirality : 0.044 0.190 4274 Planarity : 0.004 0.069 4846 Dihedral : 5.192 43.846 3826 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.02 (0.14), residues: 3504 helix: 0.45 (0.13), residues: 1586 sheet: -2.54 (0.23), residues: 420 loop : -1.26 (0.15), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 505 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.3862 time to fit residues: 324.0299 Evaluate side-chains 374 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 3.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 305 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 107 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 60 ASN ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 508 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 28452 Z= 0.170 Angle : 0.516 7.673 38466 Z= 0.270 Chirality : 0.041 0.211 4274 Planarity : 0.003 0.058 4846 Dihedral : 4.705 40.318 3826 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.54 (0.14), residues: 3504 helix: 0.94 (0.13), residues: 1594 sheet: -2.43 (0.23), residues: 420 loop : -1.09 (0.15), residues: 1490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 516 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 518 average time/residue: 0.3533 time to fit residues: 303.9977 Evaluate side-chains 396 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 2.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 0.0010 chunk 340 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 60 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 28452 Z= 0.241 Angle : 0.578 11.094 38466 Z= 0.301 Chirality : 0.042 0.214 4274 Planarity : 0.004 0.060 4846 Dihedral : 4.787 34.411 3826 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.54 (0.14), residues: 3504 helix: 0.89 (0.13), residues: 1608 sheet: -2.37 (0.24), residues: 402 loop : -1.08 (0.16), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 493 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 496 average time/residue: 0.3465 time to fit residues: 285.0678 Evaluate side-chains 375 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 286 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 339 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 107 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 28452 Z= 0.157 Angle : 0.515 9.835 38466 Z= 0.268 Chirality : 0.041 0.215 4274 Planarity : 0.003 0.059 4846 Dihedral : 4.463 34.799 3826 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.26 (0.14), residues: 3504 helix: 1.17 (0.13), residues: 1614 sheet: -2.23 (0.24), residues: 386 loop : -1.05 (0.15), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 499 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 500 average time/residue: 0.3536 time to fit residues: 295.5630 Evaluate side-chains 394 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 3.080 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2552 time to fit residues: 4.8299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 202 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 31 optimal weight: 0.0020 chunk 266 optimal weight: 0.0770 overall best weight: 0.7150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 60 ASN A 412 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 569 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 28452 Z= 0.147 Angle : 0.522 14.058 38466 Z= 0.268 Chirality : 0.041 0.233 4274 Planarity : 0.003 0.057 4846 Dihedral : 4.313 32.665 3826 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.16 (0.14), residues: 3504 helix: 1.24 (0.13), residues: 1622 sheet: -2.03 (0.24), residues: 410 loop : -1.00 (0.16), residues: 1472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 508 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 510 average time/residue: 0.3659 time to fit residues: 309.0882 Evaluate side-chains 392 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 3.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 296 optimal weight: 0.5980 chunk 316 optimal weight: 5.9990 chunk 324 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 285 optimal weight: 0.0870 chunk 299 optimal weight: 2.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 107 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 28452 Z= 0.184 Angle : 0.545 10.072 38466 Z= 0.280 Chirality : 0.041 0.212 4274 Planarity : 0.004 0.098 4846 Dihedral : 4.398 34.573 3826 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.17 (0.14), residues: 3504 helix: 1.26 (0.13), residues: 1622 sheet: -2.08 (0.24), residues: 408 loop : -1.04 (0.16), residues: 1474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 490 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 493 average time/residue: 0.3585 time to fit residues: 296.2773 Evaluate side-chains 388 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 334 optimal weight: 0.3980 chunk 204 optimal weight: 6.9990 chunk 158 optimal weight: 0.0970 chunk 232 optimal weight: 6.9990 chunk 350 optimal weight: 0.0170 chunk 322 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 28452 Z= 0.174 Angle : 0.541 9.582 38466 Z= 0.276 Chirality : 0.041 0.206 4274 Planarity : 0.004 0.090 4846 Dihedral : 4.348 34.089 3826 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.20 (0.14), residues: 3504 helix: 1.24 (0.13), residues: 1648 sheet: -2.11 (0.23), residues: 418 loop : -1.08 (0.16), residues: 1438 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 501 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 503 average time/residue: 0.3485 time to fit residues: 292.9540 Evaluate side-chains 395 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 3.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.157832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130142 restraints weight = 52817.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130205 restraints weight = 72510.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131996 restraints weight = 59930.320| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 28452 Z= 0.169 Angle : 0.537 9.219 38466 Z= 0.275 Chirality : 0.041 0.211 4274 Planarity : 0.004 0.085 4846 Dihedral : 4.326 34.460 3826 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.12 (0.14), residues: 3504 helix: 1.32 (0.13), residues: 1636 sheet: -1.99 (0.23), residues: 428 loop : -1.05 (0.16), residues: 1440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6250.55 seconds wall clock time: 114 minutes 40.83 seconds (6880.83 seconds total)