Starting phenix.real_space_refine on Tue Feb 20 12:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_24756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_24756.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_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_24756/02_2024/7rza_24756_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_24756_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_24756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_24756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_24756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rza_24756/02_2024/7rza_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 14.41, per 1000 atoms: 0.52 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: 10.52 Conformation dependent library (CDL) restraints added in 5.1 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: 6.48 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: 9.48 Time building geometry restraints manager: 11.45 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 1.177 1.412 -0.235 2.00e-02 2.50e+03 1.38e+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 - 17.76: 15939 17.76 - 35.51: 715 35.51 - 53.27: 164 53.27 - 71.03: 22 71.03 - 88.79: 14 Dihedral angle restraints: 16854 sinusoidal: 6692 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 16851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3211 0.054 - 0.109: 865 0.109 - 0.163: 166 0.163 - 0.218: 22 0.218 - 0.272: 6 Chirality restraints: 4270 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 4267 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.820 Check model and map are aligned: 0.390 Set scattering table: 0.270 Process input model: 71.660 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.160 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.830 ------------------------------------------------------------------------------- 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 4270 Planarity : 0.006 0.076 4846 Dihedral : 11.526 88.785 10332 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 % Allowed : 5.69 % Favored : 93.78 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 374 HIS 0.012 0.003 HIS D 219 PHE 0.030 0.003 PHE C 56 TYR 0.032 0.003 TYR A 218 ARG 0.015 0.001 ARG A 599 *********************** 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 : 3.322 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: A 79 LYS cc_start: 0.8977 (tptt) cc_final: 0.8770 (tppt) REVERT: A 95 SER cc_start: 0.8907 (m) cc_final: 0.8443 (p) REVERT: A 111 ILE cc_start: 0.8939 (mp) cc_final: 0.8569 (mm) REVERT: A 174 ASP cc_start: 0.5921 (p0) cc_final: 0.5652 (p0) REVERT: A 293 THR cc_start: 0.8233 (m) cc_final: 0.8031 (t) REVERT: A 359 ASN cc_start: 0.8053 (m-40) cc_final: 0.7712 (m-40) REVERT: A 373 TYR cc_start: 0.8180 (p90) cc_final: 0.7865 (p90) REVERT: A 393 LYS cc_start: 0.8632 (ttpm) cc_final: 0.8377 (ttmm) REVERT: A 435 HIS cc_start: 0.6893 (t-90) cc_final: 0.6671 (t-170) REVERT: A 527 MET cc_start: 0.7447 (mmp) cc_final: 0.7071 (mmm) REVERT: A 720 THR cc_start: 0.7631 (p) cc_final: 0.7277 (p) REVERT: A 766 TRP cc_start: 0.6540 (t-100) cc_final: 0.6044 (m100) REVERT: A 1088 LEU cc_start: 0.7288 (pp) cc_final: 0.6956 (mm) REVERT: A 1096 TRP cc_start: 0.6714 (m100) cc_final: 0.6487 (m-10) REVERT: B 185 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7068 (tp30) REVERT: B 296 PHE cc_start: 0.7563 (m-80) cc_final: 0.7264 (m-10) REVERT: B 358 ILE cc_start: 0.8563 (mt) cc_final: 0.8355 (mt) REVERT: B 503 MET cc_start: 0.7706 (ttp) cc_final: 0.7372 (tmm) REVERT: B 533 TYR cc_start: 0.7079 (t80) cc_final: 0.6873 (t80) REVERT: B 585 MET cc_start: 0.9176 (mmt) cc_final: 0.8927 (mmt) REVERT: B 612 ILE cc_start: 0.8883 (mm) cc_final: 0.8594 (tp) REVERT: B 619 ASN cc_start: 0.8130 (t0) cc_final: 0.7914 (t0) REVERT: B 667 PHE cc_start: 0.7349 (m-10) cc_final: 0.7067 (m-80) REVERT: C 140 ASP cc_start: 0.7847 (m-30) cc_final: 0.6938 (t0) REVERT: C 174 ASP cc_start: 0.5844 (p0) cc_final: 0.5639 (p0) REVERT: C 197 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6793 (tt0) REVERT: C 287 ASP cc_start: 0.7981 (m-30) cc_final: 0.7634 (m-30) REVERT: C 330 GLU cc_start: 0.8054 (pt0) cc_final: 0.7700 (pm20) REVERT: C 349 GLN cc_start: 0.7519 (pp30) cc_final: 0.7082 (pp30) REVERT: C 359 ASN cc_start: 0.8010 (m-40) cc_final: 0.7489 (m-40) REVERT: C 361 MET cc_start: 0.7111 (mtp) cc_final: 0.6896 (mtp) REVERT: C 427 ASP cc_start: 0.8115 (m-30) cc_final: 0.7591 (t70) REVERT: C 435 HIS cc_start: 0.7014 (t-90) cc_final: 0.6744 (t-170) REVERT: C 543 VAL cc_start: 0.8265 (t) cc_final: 0.8052 (p) REVERT: C 607 PHE cc_start: 0.8686 (t80) cc_final: 0.8446 (t80) REVERT: C 610 LEU cc_start: 0.9369 (tt) cc_final: 0.8965 (tp) REVERT: C 1186 GLN cc_start: 0.7913 (tt0) cc_final: 0.7606 (tt0) REVERT: C 1196 PRO cc_start: 0.6138 (Cg_exo) cc_final: 0.5935 (Cg_endo) REVERT: D 168 ILE cc_start: 0.8333 (mm) cc_final: 0.8127 (mm) REVERT: D 185 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6921 (tp30) REVERT: D 503 MET cc_start: 0.7680 (ttp) cc_final: 0.7306 (tmm) REVERT: D 538 VAL cc_start: 0.8706 (t) cc_final: 0.8493 (p) REVERT: D 585 MET cc_start: 0.9158 (mmt) cc_final: 0.8566 (mmt) REVERT: D 612 ILE cc_start: 0.8816 (mm) cc_final: 0.8588 (tp) REVERT: D 765 LYS cc_start: 0.7682 (tmmm) cc_final: 0.7470 (ttpt) REVERT: D 791 ASN cc_start: 0.8383 (m110) cc_final: 0.8151 (m110) REVERT: D 803 LEU cc_start: 0.9311 (mt) cc_final: 0.9086 (mt) outliers start: 16 outliers final: 2 residues processed: 859 average time/residue: 0.4021 time to fit residues: 533.4868 Evaluate side-chains 488 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 486 time to evaluate : 3.048 ------------------------------------------------------------------------------- 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 359 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** A1092 HIS A1152 HIS A1202 HIS B 46 HIS B 246 GLN B 274 HIS C 159 GLN C 246 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** C1092 HIS C1202 HIS D 46 HIS D 207 GLN D 246 GLN D 274 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28452 Z= 0.193 Angle : 0.581 10.698 38466 Z= 0.310 Chirality : 0.042 0.277 4270 Planarity : 0.005 0.081 4846 Dihedral : 6.531 67.176 3854 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % 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: -2.31 (0.12), residues: 3504 helix: -1.14 (0.11), residues: 1636 sheet: -2.37 (0.22), residues: 438 loop : -1.53 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 158 HIS 0.005 0.001 HIS A 46 PHE 0.027 0.002 PHE B 133 TYR 0.017 0.001 TYR A 711 ARG 0.006 0.000 ARG C 300 *********************** 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 622 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 620 time to evaluate : 3.285 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: A 95 SER cc_start: 0.8964 (m) cc_final: 0.8491 (p) REVERT: A 140 ASP cc_start: 0.7953 (m-30) cc_final: 0.7193 (t70) REVERT: A 174 ASP cc_start: 0.5735 (p0) cc_final: 0.5461 (p0) REVERT: A 408 MET cc_start: 0.6953 (tpp) cc_final: 0.6736 (tpt) REVERT: A 427 ASP cc_start: 0.8366 (m-30) cc_final: 0.8041 (t70) REVERT: A 463 MET cc_start: 0.8514 (ttp) cc_final: 0.7920 (ttp) REVERT: A 634 GLU cc_start: 0.7847 (pp20) cc_final: 0.7174 (pp20) REVERT: A 668 ASP cc_start: 0.8468 (m-30) cc_final: 0.8254 (m-30) REVERT: A 1088 LEU cc_start: 0.7092 (pp) cc_final: 0.6537 (mt) REVERT: A 1178 MET cc_start: 0.8318 (ttp) cc_final: 0.7840 (ttp) REVERT: B 42 ARG cc_start: 0.6457 (ptm160) cc_final: 0.5636 (mtt90) REVERT: B 46 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5977 (t-170) REVERT: B 325 GLN cc_start: 0.8184 (pm20) cc_final: 0.7861 (pm20) REVERT: B 363 LEU cc_start: 0.8617 (tp) cc_final: 0.8342 (tt) REVERT: B 585 MET cc_start: 0.9157 (mmt) cc_final: 0.8384 (mmt) REVERT: C 78 ASP cc_start: 0.7556 (t0) cc_final: 0.6567 (t0) REVERT: C 140 ASP cc_start: 0.7639 (m-30) cc_final: 0.6844 (t0) REVERT: C 195 ASP cc_start: 0.7875 (t70) cc_final: 0.7397 (t0) REVERT: C 304 ILE cc_start: 0.7923 (mt) cc_final: 0.7662 (mt) REVERT: C 361 MET cc_start: 0.7016 (mtp) cc_final: 0.6776 (mtp) REVERT: C 373 TYR cc_start: 0.7771 (p90) cc_final: 0.7378 (p90) REVERT: C 427 ASP cc_start: 0.8416 (m-30) cc_final: 0.8085 (t70) REVERT: C 463 MET cc_start: 0.8442 (ttp) cc_final: 0.7887 (ttp) REVERT: C 607 PHE cc_start: 0.8658 (t80) cc_final: 0.8306 (t80) REVERT: C 610 LEU cc_start: 0.9337 (tt) cc_final: 0.8964 (tp) REVERT: C 1088 LEU cc_start: 0.5486 (mm) cc_final: 0.5253 (mt) REVERT: C 1178 MET cc_start: 0.8398 (ttp) cc_final: 0.7285 (ttp) REVERT: C 1186 GLN cc_start: 0.7975 (tt0) cc_final: 0.7641 (tt0) REVERT: D 42 ARG cc_start: 0.6192 (ptm160) cc_final: 0.5657 (mtt90) REVERT: D 46 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.5991 (t-90) REVERT: D 228 THR cc_start: 0.8554 (p) cc_final: 0.8207 (t) REVERT: D 330 GLU cc_start: 0.7687 (pp20) cc_final: 0.7470 (pp20) REVERT: D 585 MET cc_start: 0.9180 (mmt) cc_final: 0.8312 (mmt) REVERT: D 791 ASN cc_start: 0.8648 (m110) cc_final: 0.8342 (m110) outliers start: 2 outliers final: 0 residues processed: 622 average time/residue: 0.3568 time to fit residues: 358.7373 Evaluate side-chains 442 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 440 time to evaluate : 3.036 ------------------------------------------------------------------------------- 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: 0.0070 chunk 99 optimal weight: 0.0970 chunk 266 optimal weight: 0.0050 chunk 217 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 0.7980 chunk 345 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 317 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 overall best weight: 0.3210 ------------------------------------------------------------------------------- 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** ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 HIS B 24 GLN B 107 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 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** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3871 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= 0.138 Angle : 0.504 7.306 38466 Z= 0.264 Chirality : 0.040 0.198 4270 Planarity : 0.004 0.064 4846 Dihedral : 5.687 70.201 3854 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: -1.30 (0.13), residues: 3504 helix: 0.05 (0.12), residues: 1642 sheet: -2.25 (0.22), residues: 450 loop : -1.35 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 158 HIS 0.003 0.001 HIS B 214 PHE 0.025 0.001 PHE C1022 TYR 0.016 0.001 TYR D 732 ARG 0.006 0.000 ARG C 300 *********************** 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 586 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 586 time to evaluate : 3.223 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: A 33 MET cc_start: 0.6979 (mmm) cc_final: 0.6716 (mmt) REVERT: A 95 SER cc_start: 0.8963 (m) cc_final: 0.8527 (p) REVERT: A 140 ASP cc_start: 0.7887 (m-30) cc_final: 0.7428 (t70) REVERT: A 174 ASP cc_start: 0.5870 (p0) cc_final: 0.5637 (p0) REVERT: A 195 ASP cc_start: 0.7860 (t70) cc_final: 0.7415 (t0) REVERT: A 408 MET cc_start: 0.7143 (tpp) cc_final: 0.6748 (tpt) REVERT: A 427 ASP cc_start: 0.8516 (m-30) cc_final: 0.8240 (m-30) REVERT: A 463 MET cc_start: 0.8531 (ttp) cc_final: 0.7877 (ttp) REVERT: A 519 ASP cc_start: 0.8515 (m-30) cc_final: 0.8111 (m-30) REVERT: A 607 PHE cc_start: 0.8449 (t80) cc_final: 0.7890 (t80) REVERT: A 732 TYR cc_start: 0.6745 (m-10) cc_final: 0.6338 (m-80) REVERT: A 1124 VAL cc_start: 0.7959 (t) cc_final: 0.7624 (t) REVERT: A 1178 MET cc_start: 0.8239 (ttp) cc_final: 0.7594 (ttp) REVERT: A 1183 MET cc_start: 0.7814 (mmm) cc_final: 0.7584 (mmm) REVERT: B 42 ARG cc_start: 0.6442 (ptm160) cc_final: 0.5657 (mtt90) REVERT: B 113 MET cc_start: 0.8642 (mmm) cc_final: 0.8345 (mmm) REVERT: B 197 GLU cc_start: 0.7732 (tp30) cc_final: 0.7289 (pm20) REVERT: B 325 GLN cc_start: 0.7996 (pm20) cc_final: 0.7725 (pm20) REVERT: B 380 MET cc_start: 0.7507 (mmm) cc_final: 0.6200 (mmm) REVERT: B 503 MET cc_start: 0.7763 (tmm) cc_final: 0.7460 (tmm) REVERT: B 504 ILE cc_start: 0.8643 (pt) cc_final: 0.8374 (pt) REVERT: B 585 MET cc_start: 0.9110 (mmt) cc_final: 0.8884 (mmt) REVERT: B 619 ASN cc_start: 0.8364 (t0) cc_final: 0.7987 (t0) REVERT: B 789 LEU cc_start: 0.7256 (tp) cc_final: 0.6721 (mp) REVERT: C 78 ASP cc_start: 0.7704 (t0) cc_final: 0.6783 (t0) REVERT: C 95 SER cc_start: 0.8943 (m) cc_final: 0.8368 (p) REVERT: C 132 LYS cc_start: 0.7890 (tptp) cc_final: 0.7622 (tppt) REVERT: C 140 ASP cc_start: 0.7719 (m-30) cc_final: 0.7048 (t70) REVERT: C 195 ASP cc_start: 0.7767 (t70) cc_final: 0.7501 (t0) REVERT: C 361 MET cc_start: 0.6918 (mtp) cc_final: 0.6657 (mtp) REVERT: C 413 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6760 (tm-30) REVERT: C 427 ASP cc_start: 0.8478 (m-30) cc_final: 0.8115 (t70) REVERT: C 435 HIS cc_start: 0.6858 (t-90) cc_final: 0.6629 (t-90) REVERT: C 443 THR cc_start: 0.7879 (t) cc_final: 0.7534 (t) REVERT: C 463 MET cc_start: 0.8413 (ttp) cc_final: 0.7820 (ttp) REVERT: C 519 ASP cc_start: 0.8515 (m-30) cc_final: 0.8200 (m-30) REVERT: C 585 MET cc_start: 0.8316 (mmp) cc_final: 0.7724 (mmt) REVERT: C 607 PHE cc_start: 0.8567 (t80) cc_final: 0.8243 (t80) REVERT: C 610 LEU cc_start: 0.9205 (tt) cc_final: 0.8804 (tp) REVERT: C 1088 LEU cc_start: 0.5580 (mm) cc_final: 0.4564 (pt) REVERT: C 1178 MET cc_start: 0.8375 (ttp) cc_final: 0.7181 (ttp) REVERT: C 1182 MET cc_start: 0.7670 (mmp) cc_final: 0.7430 (mmt) REVERT: D 42 ARG cc_start: 0.6158 (ptm160) cc_final: 0.5637 (mtt90) REVERT: D 85 ILE cc_start: 0.8729 (mm) cc_final: 0.8528 (mm) REVERT: D 131 ASP cc_start: 0.7806 (p0) cc_final: 0.7425 (p0) REVERT: D 185 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7179 (tp30) REVERT: D 228 THR cc_start: 0.8573 (p) cc_final: 0.8166 (t) REVERT: D 330 GLU cc_start: 0.7753 (pp20) cc_final: 0.7505 (pp20) REVERT: D 503 MET cc_start: 0.7687 (tmm) cc_final: 0.7375 (tmm) REVERT: D 504 ILE cc_start: 0.8516 (pt) cc_final: 0.8284 (pt) REVERT: D 585 MET cc_start: 0.9075 (mmt) cc_final: 0.8352 (mmt) REVERT: D 791 ASN cc_start: 0.8613 (m110) cc_final: 0.8232 (m110) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.3651 time to fit residues: 348.1092 Evaluate side-chains 422 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.027 ------------------------------------------------------------------------------- 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: 0.7980 chunk 240 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 152 optimal weight: 0.0370 chunk 215 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 304 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 2.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 214 HIS B 298 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS ** 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28452 Z= 0.276 Angle : 0.611 8.809 38466 Z= 0.321 Chirality : 0.043 0.194 4270 Planarity : 0.004 0.069 4846 Dihedral : 6.184 74.492 3854 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % 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: -0.97 (0.14), residues: 3504 helix: 0.45 (0.13), residues: 1606 sheet: -2.48 (0.23), residues: 418 loop : -1.21 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 158 HIS 0.011 0.001 HIS C 412 PHE 0.023 0.002 PHE B 133 TYR 0.016 0.002 TYR B 405 ARG 0.006 0.000 ARG A 114 *********************** 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 501 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 499 time to evaluate : 2.960 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: A 25 GLU cc_start: 0.8379 (mp0) cc_final: 0.8118 (mp0) REVERT: A 33 MET cc_start: 0.7442 (mmm) cc_final: 0.7131 (mmt) REVERT: A 43 LEU cc_start: 0.8710 (mt) cc_final: 0.8389 (mt) REVERT: A 79 LYS cc_start: 0.9147 (tptt) cc_final: 0.8814 (tppt) REVERT: A 95 SER cc_start: 0.8933 (m) cc_final: 0.8452 (p) REVERT: A 140 ASP cc_start: 0.7938 (m-30) cc_final: 0.7249 (t0) REVERT: A 218 TYR cc_start: 0.7526 (m-80) cc_final: 0.6843 (m-80) REVERT: A 427 ASP cc_start: 0.8486 (m-30) cc_final: 0.8274 (m-30) REVERT: A 463 MET cc_start: 0.8663 (ttp) cc_final: 0.7656 (ttp) REVERT: A 634 GLU cc_start: 0.7807 (pp20) cc_final: 0.7183 (pp20) REVERT: A 668 ASP cc_start: 0.8489 (m-30) cc_final: 0.8224 (m-30) REVERT: A 1008 ARG cc_start: 0.5662 (mmt180) cc_final: 0.5032 (mtt90) REVERT: A 1178 MET cc_start: 0.8353 (ttp) cc_final: 0.7778 (ttp) REVERT: B 46 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.5862 (t70) REVERT: B 85 ILE cc_start: 0.8738 (mm) cc_final: 0.8512 (mm) REVERT: B 380 MET cc_start: 0.7547 (mmm) cc_final: 0.6810 (mmm) REVERT: B 407 MET cc_start: 0.7556 (mmm) cc_final: 0.7126 (mmp) REVERT: B 503 MET cc_start: 0.7653 (tmm) cc_final: 0.7244 (tmm) REVERT: B 504 ILE cc_start: 0.8667 (pt) cc_final: 0.8384 (pt) REVERT: B 585 MET cc_start: 0.9200 (mmt) cc_final: 0.8281 (mmt) REVERT: B 720 THR cc_start: 0.8074 (p) cc_final: 0.7834 (p) REVERT: B 770 LYS cc_start: 0.3225 (tptm) cc_final: 0.2649 (mmtp) REVERT: C 78 ASP cc_start: 0.7574 (t0) cc_final: 0.6461 (t0) REVERT: C 95 SER cc_start: 0.8829 (m) cc_final: 0.8272 (p) REVERT: C 113 MET cc_start: 0.8404 (mmm) cc_final: 0.8196 (ttm) REVERT: C 140 ASP cc_start: 0.7841 (m-30) cc_final: 0.7069 (t0) REVERT: C 195 ASP cc_start: 0.7795 (t70) cc_final: 0.7487 (p0) REVERT: C 218 TYR cc_start: 0.7543 (m-80) cc_final: 0.6982 (m-80) REVERT: C 361 MET cc_start: 0.6945 (mtp) cc_final: 0.6597 (mtp) REVERT: C 427 ASP cc_start: 0.8441 (m-30) cc_final: 0.8127 (t70) REVERT: C 463 MET cc_start: 0.8598 (ttp) cc_final: 0.8163 (ttp) REVERT: C 607 PHE cc_start: 0.8781 (t80) cc_final: 0.8398 (t80) REVERT: C 610 LEU cc_start: 0.9377 (tt) cc_final: 0.9005 (tp) REVERT: C 634 GLU cc_start: 0.7836 (pp20) cc_final: 0.7525 (pp20) REVERT: C 668 ASP cc_start: 0.8448 (m-30) cc_final: 0.8218 (m-30) REVERT: C 1088 LEU cc_start: 0.5397 (mm) cc_final: 0.5187 (mt) REVERT: D 42 ARG cc_start: 0.6700 (ptm160) cc_final: 0.5840 (mtt90) REVERT: D 85 ILE cc_start: 0.8852 (mm) cc_final: 0.8624 (mm) REVERT: D 330 GLU cc_start: 0.7798 (pp20) cc_final: 0.7393 (pp20) REVERT: D 503 MET cc_start: 0.7579 (tmm) cc_final: 0.7202 (tmm) REVERT: D 504 ILE cc_start: 0.8568 (pt) cc_final: 0.8316 (pt) REVERT: D 580 SER cc_start: 0.8723 (m) cc_final: 0.8521 (p) REVERT: D 585 MET cc_start: 0.9231 (mmt) cc_final: 0.8406 (mmt) REVERT: D 791 ASN cc_start: 0.8660 (m110) cc_final: 0.8240 (m110) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.3919 time to fit residues: 321.5871 Evaluate side-chains 389 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 3.138 ------------------------------------------------------------------------------- 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: 2.9990 chunk 193 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 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 107 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 359 ASN ** 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 359 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28452 Z= 0.223 Angle : 0.547 8.294 38466 Z= 0.286 Chirality : 0.041 0.210 4270 Planarity : 0.004 0.062 4846 Dihedral : 6.206 89.048 3854 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.10 % 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: -0.62 (0.14), residues: 3504 helix: 0.83 (0.13), residues: 1596 sheet: -2.44 (0.23), residues: 420 loop : -1.09 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 158 HIS 0.007 0.001 HIS C 412 PHE 0.025 0.002 PHE D 623 TYR 0.018 0.001 TYR C 702 ARG 0.003 0.000 ARG B 178 *********************** 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 514 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 3.447 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: A 25 GLU cc_start: 0.8336 (mp0) cc_final: 0.8087 (mp0) REVERT: A 33 MET cc_start: 0.7587 (mmm) cc_final: 0.7268 (mmm) REVERT: A 78 ASP cc_start: 0.7656 (t0) cc_final: 0.6478 (t0) REVERT: A 95 SER cc_start: 0.8952 (m) cc_final: 0.8517 (p) REVERT: A 140 ASP cc_start: 0.7869 (m-30) cc_final: 0.7301 (t70) REVERT: A 189 GLU cc_start: 0.7272 (tp30) cc_final: 0.7050 (tp30) REVERT: A 218 TYR cc_start: 0.7584 (m-80) cc_final: 0.7036 (m-80) REVERT: A 241 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7112 (mt-10) REVERT: A 427 ASP cc_start: 0.8430 (m-30) cc_final: 0.8227 (m-30) REVERT: A 463 MET cc_start: 0.8667 (ttp) cc_final: 0.8114 (ttp) REVERT: A 519 ASP cc_start: 0.8542 (m-30) cc_final: 0.8161 (m-30) REVERT: A 634 GLU cc_start: 0.7753 (pp20) cc_final: 0.7154 (pp20) REVERT: A 668 ASP cc_start: 0.8461 (m-30) cc_final: 0.8210 (m-30) REVERT: A 1178 MET cc_start: 0.8302 (ttp) cc_final: 0.7894 (ttp) REVERT: B 380 MET cc_start: 0.7597 (mmm) cc_final: 0.6855 (mmm) REVERT: B 407 MET cc_start: 0.7511 (mmm) cc_final: 0.6940 (mmp) REVERT: B 503 MET cc_start: 0.7385 (tmm) cc_final: 0.7034 (tmm) REVERT: B 585 MET cc_start: 0.9194 (mmt) cc_final: 0.8433 (mmt) REVERT: B 720 THR cc_start: 0.8021 (p) cc_final: 0.7804 (p) REVERT: B 770 LYS cc_start: 0.3306 (tptm) cc_final: 0.2513 (mmtp) REVERT: C 78 ASP cc_start: 0.7482 (t0) cc_final: 0.6571 (t0) REVERT: C 95 SER cc_start: 0.8782 (m) cc_final: 0.8249 (p) REVERT: C 140 ASP cc_start: 0.7708 (m-30) cc_final: 0.6990 (t70) REVERT: C 195 ASP cc_start: 0.7826 (t70) cc_final: 0.7449 (p0) REVERT: C 218 TYR cc_start: 0.7536 (m-80) cc_final: 0.6979 (m-80) REVERT: C 361 MET cc_start: 0.7025 (mtp) cc_final: 0.6661 (mtp) REVERT: C 427 ASP cc_start: 0.8397 (m-30) cc_final: 0.8164 (m-30) REVERT: C 435 HIS cc_start: 0.7068 (t-90) cc_final: 0.6720 (t-90) REVERT: C 463 MET cc_start: 0.8573 (ttp) cc_final: 0.8019 (ttp) REVERT: C 519 ASP cc_start: 0.8443 (m-30) cc_final: 0.8110 (m-30) REVERT: C 607 PHE cc_start: 0.8751 (t80) cc_final: 0.8351 (t80) REVERT: C 610 LEU cc_start: 0.9322 (tt) cc_final: 0.8970 (tp) REVERT: C 634 GLU cc_start: 0.7883 (pp20) cc_final: 0.7527 (pp20) REVERT: C 668 ASP cc_start: 0.8443 (m-30) cc_final: 0.8208 (m-30) REVERT: C 759 LEU cc_start: 0.8419 (mt) cc_final: 0.8158 (mt) REVERT: C 1088 LEU cc_start: 0.5266 (mm) cc_final: 0.5035 (mt) REVERT: C 1183 MET cc_start: 0.7886 (mmm) cc_final: 0.7512 (mmm) REVERT: D 113 MET cc_start: 0.8508 (mmm) cc_final: 0.8222 (mmm) REVERT: D 131 ASP cc_start: 0.7683 (p0) cc_final: 0.7211 (p0) REVERT: D 185 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7167 (tp30) REVERT: D 330 GLU cc_start: 0.7794 (pp20) cc_final: 0.7386 (pp20) REVERT: D 407 MET cc_start: 0.7419 (mmm) cc_final: 0.6896 (mmp) REVERT: D 503 MET cc_start: 0.7433 (tmm) cc_final: 0.7186 (tmm) REVERT: D 585 MET cc_start: 0.9218 (mmt) cc_final: 0.8321 (mmt) REVERT: D 770 LYS cc_start: 0.3144 (tptm) cc_final: 0.2418 (mmtp) REVERT: D 791 ASN cc_start: 0.8643 (m110) cc_final: 0.8218 (m110) outliers start: 1 outliers final: 0 residues processed: 514 average time/residue: 0.3604 time to fit residues: 307.3687 Evaluate side-chains 400 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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: 2.9990 chunk 67 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 340 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 359 ASN A 508 GLN ** A 575 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 46 HIS B 107 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 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 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28452 Z= 0.200 Angle : 0.542 11.393 38466 Z= 0.281 Chirality : 0.041 0.211 4270 Planarity : 0.003 0.060 4846 Dihedral : 5.890 89.967 3854 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % 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: -0.44 (0.14), residues: 3504 helix: 0.98 (0.13), residues: 1610 sheet: -2.28 (0.24), residues: 408 loop : -1.05 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 158 HIS 0.007 0.001 HIS C 412 PHE 0.021 0.001 PHE C1022 TYR 0.018 0.001 TYR C 702 ARG 0.003 0.000 ARG C 114 *********************** 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 504 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 502 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: A 25 GLU cc_start: 0.8305 (mp0) cc_final: 0.8045 (mp0) REVERT: A 78 ASP cc_start: 0.7677 (t0) cc_final: 0.6547 (t0) REVERT: A 95 SER cc_start: 0.8908 (m) cc_final: 0.8433 (p) REVERT: A 140 ASP cc_start: 0.7955 (m-30) cc_final: 0.7383 (t70) REVERT: A 218 TYR cc_start: 0.7538 (m-80) cc_final: 0.6960 (m-80) REVERT: A 427 ASP cc_start: 0.8423 (m-30) cc_final: 0.8217 (m-30) REVERT: A 463 MET cc_start: 0.8646 (ttp) cc_final: 0.8049 (ttp) REVERT: A 668 ASP cc_start: 0.8463 (m-30) cc_final: 0.8227 (m-30) REVERT: A 759 LEU cc_start: 0.8347 (mt) cc_final: 0.7232 (tp) REVERT: B 46 HIS cc_start: 0.6003 (OUTLIER) cc_final: 0.5783 (t70) REVERT: B 85 ILE cc_start: 0.8700 (mm) cc_final: 0.8490 (mm) REVERT: B 380 MET cc_start: 0.7604 (mmm) cc_final: 0.6840 (mmm) REVERT: B 407 MET cc_start: 0.7486 (mmm) cc_final: 0.7030 (mmp) REVERT: B 503 MET cc_start: 0.7198 (tmm) cc_final: 0.6754 (tmm) REVERT: B 585 MET cc_start: 0.9161 (mmt) cc_final: 0.8441 (mmt) REVERT: B 770 LYS cc_start: 0.3415 (tptm) cc_final: 0.2467 (mmtp) REVERT: C 65 GLN cc_start: 0.8419 (mp10) cc_final: 0.7888 (mp10) REVERT: C 78 ASP cc_start: 0.7577 (t0) cc_final: 0.6715 (t0) REVERT: C 95 SER cc_start: 0.8758 (m) cc_final: 0.8298 (p) REVERT: C 113 MET cc_start: 0.8349 (mmm) cc_final: 0.8074 (mtt) REVERT: C 140 ASP cc_start: 0.7763 (m-30) cc_final: 0.7168 (t70) REVERT: C 195 ASP cc_start: 0.7876 (t70) cc_final: 0.7525 (p0) REVERT: C 361 MET cc_start: 0.6961 (mtp) cc_final: 0.6523 (mtp) REVERT: C 405 TYR cc_start: 0.7772 (m-80) cc_final: 0.7516 (m-80) REVERT: C 427 ASP cc_start: 0.8378 (m-30) cc_final: 0.8040 (t70) REVERT: C 435 HIS cc_start: 0.7028 (t-90) cc_final: 0.6750 (t-90) REVERT: C 463 MET cc_start: 0.8587 (ttp) cc_final: 0.7986 (ttp) REVERT: C 607 PHE cc_start: 0.8761 (t80) cc_final: 0.8333 (t80) REVERT: C 610 LEU cc_start: 0.9327 (tt) cc_final: 0.8961 (tp) REVERT: C 634 GLU cc_start: 0.7791 (pp20) cc_final: 0.7461 (pp20) REVERT: C 668 ASP cc_start: 0.8395 (m-30) cc_final: 0.8165 (m-30) REVERT: C 674 MET cc_start: 0.7994 (mtm) cc_final: 0.7712 (mtm) REVERT: C 759 LEU cc_start: 0.8344 (mt) cc_final: 0.8133 (mt) REVERT: C 1088 LEU cc_start: 0.5307 (mm) cc_final: 0.5066 (mt) REVERT: D 46 HIS cc_start: 0.5885 (OUTLIER) cc_final: 0.5662 (t-90) REVERT: D 85 ILE cc_start: 0.8785 (mm) cc_final: 0.8530 (mm) REVERT: D 185 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7147 (tp30) REVERT: D 407 MET cc_start: 0.7443 (mmm) cc_final: 0.6757 (mmp) REVERT: D 503 MET cc_start: 0.7120 (tmm) cc_final: 0.6820 (tmm) REVERT: D 585 MET cc_start: 0.9177 (mmt) cc_final: 0.8194 (mmt) REVERT: D 720 THR cc_start: 0.8006 (p) cc_final: 0.7784 (p) REVERT: D 770 LYS cc_start: 0.3025 (tptm) cc_final: 0.2193 (mmtp) REVERT: D 791 ASN cc_start: 0.8615 (m110) cc_final: 0.8165 (m110) outliers start: 2 outliers final: 0 residues processed: 504 average time/residue: 0.3476 time to fit residues: 290.6563 Evaluate side-chains 399 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 397 time to evaluate : 2.905 ------------------------------------------------------------------------------- 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: 0.6980 chunk 38 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 286 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 359 ASN ** A 575 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 107 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 359 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** D 107 HIS D 337 GLN ** D 359 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28452 Z= 0.249 Angle : 0.576 9.811 38466 Z= 0.300 Chirality : 0.042 0.209 4270 Planarity : 0.004 0.060 4846 Dihedral : 5.699 85.525 3854 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.94 % 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: -0.49 (0.14), residues: 3504 helix: 0.94 (0.13), residues: 1610 sheet: -2.38 (0.24), residues: 402 loop : -1.05 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C1032 HIS 0.007 0.001 HIS C 412 PHE 0.018 0.002 PHE B 133 TYR 0.019 0.002 TYR A 533 ARG 0.004 0.000 ARG A 114 *********************** 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 490 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 3.048 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: A 25 GLU cc_start: 0.8254 (mp0) cc_final: 0.7997 (mp0) REVERT: A 78 ASP cc_start: 0.7660 (t0) cc_final: 0.6454 (t0) REVERT: A 95 SER cc_start: 0.8876 (m) cc_final: 0.8431 (p) REVERT: A 132 LYS cc_start: 0.8318 (tptm) cc_final: 0.7809 (tppt) REVERT: A 140 ASP cc_start: 0.7940 (m-30) cc_final: 0.7385 (t70) REVERT: A 218 TYR cc_start: 0.7413 (m-80) cc_final: 0.6970 (m-80) REVERT: A 463 MET cc_start: 0.8663 (ttp) cc_final: 0.8117 (ttp) REVERT: A 668 ASP cc_start: 0.8518 (m-30) cc_final: 0.8271 (m-30) REVERT: B 380 MET cc_start: 0.7677 (mmm) cc_final: 0.6970 (mmm) REVERT: B 407 MET cc_start: 0.7487 (mmm) cc_final: 0.6990 (mmp) REVERT: B 585 MET cc_start: 0.9171 (mmt) cc_final: 0.8420 (mmt) REVERT: B 720 THR cc_start: 0.8201 (p) cc_final: 0.7953 (p) REVERT: B 770 LYS cc_start: 0.3369 (tptm) cc_final: 0.2262 (mmtp) REVERT: C 33 MET cc_start: 0.7802 (mmm) cc_final: 0.7564 (mmt) REVERT: C 65 GLN cc_start: 0.8500 (mp10) cc_final: 0.8115 (mp10) REVERT: C 78 ASP cc_start: 0.7553 (t0) cc_final: 0.6717 (t0) REVERT: C 95 SER cc_start: 0.8728 (m) cc_final: 0.8279 (p) REVERT: C 140 ASP cc_start: 0.7777 (m-30) cc_final: 0.7191 (t70) REVERT: C 147 GLN cc_start: 0.8318 (mt0) cc_final: 0.8097 (mt0) REVERT: C 195 ASP cc_start: 0.7928 (t70) cc_final: 0.7617 (p0) REVERT: C 361 MET cc_start: 0.6964 (mtp) cc_final: 0.6509 (mtp) REVERT: C 427 ASP cc_start: 0.8383 (m-30) cc_final: 0.8090 (t70) REVERT: C 435 HIS cc_start: 0.7074 (t-90) cc_final: 0.6808 (t-90) REVERT: C 463 MET cc_start: 0.8602 (ttp) cc_final: 0.7630 (ttp) REVERT: C 519 ASP cc_start: 0.8492 (m-30) cc_final: 0.8183 (m-30) REVERT: C 607 PHE cc_start: 0.8786 (t80) cc_final: 0.8379 (t80) REVERT: C 610 LEU cc_start: 0.9372 (tt) cc_final: 0.9036 (tp) REVERT: C 668 ASP cc_start: 0.8412 (m-30) cc_final: 0.8185 (m-30) REVERT: C 1183 MET cc_start: 0.7825 (mmm) cc_final: 0.7563 (mmm) REVERT: D 85 ILE cc_start: 0.8799 (mm) cc_final: 0.8568 (mm) REVERT: D 113 MET cc_start: 0.8449 (mmm) cc_final: 0.8152 (mmm) REVERT: D 185 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7117 (tp30) REVERT: D 361 MET cc_start: 0.8894 (mtp) cc_final: 0.8628 (mtm) REVERT: D 580 SER cc_start: 0.8748 (m) cc_final: 0.8507 (p) REVERT: D 585 MET cc_start: 0.9223 (mmt) cc_final: 0.8370 (mmt) REVERT: D 641 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8327 (mptt) REVERT: D 720 THR cc_start: 0.8167 (p) cc_final: 0.7841 (p) REVERT: D 770 LYS cc_start: 0.3264 (tptm) cc_final: 0.2190 (mmtp) REVERT: D 791 ASN cc_start: 0.8639 (m110) cc_final: 0.8182 (m110) outliers start: 2 outliers final: 0 residues processed: 490 average time/residue: 0.3524 time to fit residues: 286.3882 Evaluate side-chains 392 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 3.121 ------------------------------------------------------------------------------- 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: 7.9990 chunk 135 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 215 optimal weight: 7.9990 chunk 231 optimal weight: 0.2980 chunk 167 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 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** D 46 HIS D 337 GLN ** D 359 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28452 Z= 0.220 Angle : 0.573 13.441 38466 Z= 0.297 Chirality : 0.042 0.234 4270 Planarity : 0.004 0.096 4846 Dihedral : 5.337 72.043 3854 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.13 % Allowed : 0.73 % Favored : 99.14 % 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: -0.44 (0.14), residues: 3504 helix: 1.01 (0.13), residues: 1616 sheet: -2.36 (0.24), residues: 410 loop : -1.07 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 158 HIS 0.005 0.001 HIS C 412 PHE 0.017 0.002 PHE B 133 TYR 0.017 0.001 TYR C 702 ARG 0.009 0.000 ARG D 453 *********************** 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 488 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 484 time to evaluate : 3.051 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: A 25 GLU cc_start: 0.8242 (mp0) cc_final: 0.7977 (mp0) REVERT: A 65 GLN cc_start: 0.8484 (mp10) cc_final: 0.8268 (mp10) REVERT: A 78 ASP cc_start: 0.7595 (t0) cc_final: 0.6419 (t0) REVERT: A 95 SER cc_start: 0.8851 (m) cc_final: 0.8375 (p) REVERT: A 140 ASP cc_start: 0.7921 (m-30) cc_final: 0.7356 (t70) REVERT: A 463 MET cc_start: 0.8634 (ttp) cc_final: 0.8089 (ttp) REVERT: A 668 ASP cc_start: 0.8547 (m-30) cc_final: 0.8315 (m-30) REVERT: A 759 LEU cc_start: 0.8272 (mt) cc_final: 0.7131 (tp) REVERT: A 1183 MET cc_start: 0.7919 (mmm) cc_final: 0.7615 (mmm) REVERT: B 46 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.5670 (t70) REVERT: B 85 ILE cc_start: 0.8710 (mm) cc_final: 0.8463 (mm) REVERT: B 195 ASP cc_start: 0.8377 (t0) cc_final: 0.8167 (t0) REVERT: B 380 MET cc_start: 0.7660 (mmm) cc_final: 0.6959 (mmm) REVERT: B 407 MET cc_start: 0.7471 (mmm) cc_final: 0.7257 (mmp) REVERT: B 585 MET cc_start: 0.9169 (mmt) cc_final: 0.8454 (mmt) REVERT: B 708 MET cc_start: 0.6785 (ptp) cc_final: 0.6371 (ptp) REVERT: B 720 THR cc_start: 0.8086 (p) cc_final: 0.7859 (p) REVERT: B 770 LYS cc_start: 0.3392 (tptm) cc_final: 0.2390 (mmtt) REVERT: B 791 ASN cc_start: 0.8548 (m-40) cc_final: 0.8246 (m-40) REVERT: C 33 MET cc_start: 0.7753 (mmm) cc_final: 0.7512 (mmt) REVERT: C 65 GLN cc_start: 0.8471 (mp10) cc_final: 0.7847 (mp10) REVERT: C 78 ASP cc_start: 0.7547 (t0) cc_final: 0.6717 (t0) REVERT: C 95 SER cc_start: 0.8721 (m) cc_final: 0.8297 (p) REVERT: C 140 ASP cc_start: 0.7766 (m-30) cc_final: 0.7186 (t70) REVERT: C 147 GLN cc_start: 0.8313 (mt0) cc_final: 0.8109 (mt0) REVERT: C 195 ASP cc_start: 0.7917 (t70) cc_final: 0.7592 (p0) REVERT: C 361 MET cc_start: 0.6955 (mtp) cc_final: 0.6462 (mtp) REVERT: C 427 ASP cc_start: 0.8345 (m-30) cc_final: 0.8067 (t70) REVERT: C 435 HIS cc_start: 0.7050 (t-90) cc_final: 0.6797 (t-90) REVERT: C 463 MET cc_start: 0.8586 (ttp) cc_final: 0.8154 (ttp) REVERT: C 533 TYR cc_start: 0.8466 (t80) cc_final: 0.8169 (t80) REVERT: C 607 PHE cc_start: 0.8778 (t80) cc_final: 0.8363 (t80) REVERT: C 610 LEU cc_start: 0.9348 (tt) cc_final: 0.8988 (tp) REVERT: C 668 ASP cc_start: 0.8424 (m-30) cc_final: 0.8182 (m-30) REVERT: C 1183 MET cc_start: 0.7872 (mmm) cc_final: 0.7566 (mmm) REVERT: D 46 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5635 (t70) REVERT: D 85 ILE cc_start: 0.8819 (mm) cc_final: 0.8567 (mm) REVERT: D 113 MET cc_start: 0.8432 (mmm) cc_final: 0.8166 (mmm) REVERT: D 185 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7125 (tp30) REVERT: D 380 MET cc_start: 0.7138 (mmm) cc_final: 0.6625 (mmm) REVERT: D 585 MET cc_start: 0.9233 (mmt) cc_final: 0.8336 (mmt) REVERT: D 720 THR cc_start: 0.8136 (p) cc_final: 0.7840 (p) REVERT: D 791 ASN cc_start: 0.8619 (m110) cc_final: 0.8126 (m110) outliers start: 4 outliers final: 1 residues processed: 488 average time/residue: 0.3414 time to fit residues: 279.9176 Evaluate side-chains 398 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 395 time to evaluate : 3.185 ------------------------------------------------------------------------------- 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: 5.9990 chunk 296 optimal weight: 0.5980 chunk 316 optimal weight: 8.9990 chunk 324 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 359 ASN ** A 575 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5482 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= 0.168 Angle : 0.537 10.052 38466 Z= 0.276 Chirality : 0.041 0.213 4270 Planarity : 0.003 0.085 4846 Dihedral : 4.658 35.773 3854 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.03 % Allowed : 0.60 % Favored : 99.37 % 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: -0.23 (0.14), residues: 3504 helix: 1.20 (0.13), residues: 1610 sheet: -2.28 (0.24), residues: 406 loop : -0.97 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C1204 HIS 0.006 0.001 HIS C 412 PHE 0.024 0.001 PHE C1210 TYR 0.019 0.001 TYR A 533 ARG 0.003 0.000 ARG A 369 *********************** 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 513 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 3.404 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: A 78 ASP cc_start: 0.7680 (t0) cc_final: 0.6554 (t0) REVERT: A 95 SER cc_start: 0.8845 (m) cc_final: 0.8324 (p) REVERT: A 140 ASP cc_start: 0.7819 (m-30) cc_final: 0.7365 (t70) REVERT: A 241 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 365 THR cc_start: 0.7802 (m) cc_final: 0.7496 (p) REVERT: A 463 MET cc_start: 0.8649 (ttp) cc_final: 0.8077 (ttp) REVERT: A 527 MET cc_start: 0.7216 (mmm) cc_final: 0.6994 (tpp) REVERT: A 607 PHE cc_start: 0.8716 (t80) cc_final: 0.7888 (t80) REVERT: A 668 ASP cc_start: 0.8537 (m-30) cc_final: 0.8307 (m-30) REVERT: A 759 LEU cc_start: 0.8288 (mt) cc_final: 0.7215 (tp) REVERT: B 183 ASP cc_start: 0.6883 (t70) cc_final: 0.6666 (t70) REVERT: B 228 THR cc_start: 0.8826 (p) cc_final: 0.8375 (t) REVERT: B 380 MET cc_start: 0.7618 (mmm) cc_final: 0.6855 (mmm) REVERT: B 407 MET cc_start: 0.7526 (mmm) cc_final: 0.7282 (mmp) REVERT: B 503 MET cc_start: 0.7743 (tmm) cc_final: 0.7387 (tmm) REVERT: B 585 MET cc_start: 0.9155 (mmt) cc_final: 0.8422 (mmt) REVERT: B 708 MET cc_start: 0.6700 (ptp) cc_final: 0.6236 (ptp) REVERT: B 791 ASN cc_start: 0.8399 (m-40) cc_final: 0.8157 (m-40) REVERT: C 65 GLN cc_start: 0.8428 (mp10) cc_final: 0.7823 (mp10) REVERT: C 78 ASP cc_start: 0.7600 (t0) cc_final: 0.6829 (t0) REVERT: C 95 SER cc_start: 0.8704 (m) cc_final: 0.8212 (p) REVERT: C 132 LYS cc_start: 0.8075 (tptm) cc_final: 0.7728 (tppt) REVERT: C 140 ASP cc_start: 0.7653 (m-30) cc_final: 0.7131 (t70) REVERT: C 147 GLN cc_start: 0.8294 (mt0) cc_final: 0.8067 (mt0) REVERT: C 195 ASP cc_start: 0.7859 (t70) cc_final: 0.7470 (p0) REVERT: C 361 MET cc_start: 0.6812 (mtp) cc_final: 0.6401 (mtp) REVERT: C 365 THR cc_start: 0.7852 (m) cc_final: 0.7569 (p) REVERT: C 401 LEU cc_start: 0.7115 (tp) cc_final: 0.6790 (pp) REVERT: C 427 ASP cc_start: 0.8314 (m-30) cc_final: 0.8054 (t70) REVERT: C 463 MET cc_start: 0.8576 (ttp) cc_final: 0.8138 (ttp) REVERT: C 496 MET cc_start: 0.7599 (ptm) cc_final: 0.7372 (ptm) REVERT: C 527 MET cc_start: 0.6986 (mmm) cc_final: 0.6535 (mpp) REVERT: C 607 PHE cc_start: 0.8724 (t80) cc_final: 0.8328 (t80) REVERT: C 1178 MET cc_start: 0.8354 (ttp) cc_final: 0.6600 (tmm) REVERT: C 1183 MET cc_start: 0.7822 (mmm) cc_final: 0.7462 (mmm) REVERT: D 113 MET cc_start: 0.8463 (mmm) cc_final: 0.8181 (mmm) REVERT: D 185 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7095 (tp30) REVERT: D 228 THR cc_start: 0.8926 (p) cc_final: 0.8459 (t) REVERT: D 380 MET cc_start: 0.7197 (mmm) cc_final: 0.6573 (mmm) REVERT: D 504 ILE cc_start: 0.8428 (pt) cc_final: 0.8194 (pt) REVERT: D 585 MET cc_start: 0.9184 (mmt) cc_final: 0.8124 (mmt) REVERT: D 791 ASN cc_start: 0.8566 (m110) cc_final: 0.8092 (m110) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.3412 time to fit residues: 292.8512 Evaluate side-chains 393 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 3.602 ------------------------------------------------------------------------------- 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: 10.0000 chunk 207 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** 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 359 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28452 Z= 0.244 Angle : 0.593 9.178 38466 Z= 0.308 Chirality : 0.043 0.207 4270 Planarity : 0.004 0.086 4846 Dihedral : 4.830 28.082 3854 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.10 % Allowed : 0.17 % Favored : 99.73 % 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: -0.39 (0.14), residues: 3504 helix: 1.07 (0.13), residues: 1622 sheet: -2.45 (0.24), residues: 404 loop : -1.05 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C1032 HIS 0.004 0.001 HIS B 219 PHE 0.016 0.002 PHE D 74 TYR 0.016 0.001 TYR C 533 ARG 0.003 0.000 ARG C 692 ********************** 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 478 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 475 time to evaluate : 3.086 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: A 25 GLU cc_start: 0.8273 (mp0) cc_final: 0.7670 (mp0) REVERT: A 95 SER cc_start: 0.8824 (m) cc_final: 0.8327 (p) REVERT: A 140 ASP cc_start: 0.7867 (m-30) cc_final: 0.7386 (t70) REVERT: A 463 MET cc_start: 0.8657 (ttp) cc_final: 0.8151 (ttp) REVERT: A 519 ASP cc_start: 0.8527 (m-30) cc_final: 0.8122 (m-30) REVERT: A 668 ASP cc_start: 0.8541 (m-30) cc_final: 0.8309 (m-30) REVERT: A 759 LEU cc_start: 0.8200 (mt) cc_final: 0.7154 (tp) REVERT: B 46 HIS cc_start: 0.5940 (OUTLIER) cc_final: 0.5706 (t70) REVERT: B 85 ILE cc_start: 0.8743 (mm) cc_final: 0.8507 (mm) REVERT: B 228 THR cc_start: 0.8920 (p) cc_final: 0.8486 (t) REVERT: B 330 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7075 (tm-30) REVERT: B 380 MET cc_start: 0.7751 (mmm) cc_final: 0.7005 (mmm) REVERT: B 407 MET cc_start: 0.7615 (mmm) cc_final: 0.7357 (mmp) REVERT: B 503 MET cc_start: 0.7621 (tmm) cc_final: 0.7253 (tmm) REVERT: B 585 MET cc_start: 0.9176 (mmt) cc_final: 0.8488 (mmt) REVERT: B 708 MET cc_start: 0.6774 (ptp) cc_final: 0.6178 (ptt) REVERT: B 791 ASN cc_start: 0.8481 (m-40) cc_final: 0.8228 (m-40) REVERT: C 65 GLN cc_start: 0.8491 (mp10) cc_final: 0.7817 (mp10) REVERT: C 78 ASP cc_start: 0.7542 (t0) cc_final: 0.6751 (t0) REVERT: C 95 SER cc_start: 0.8682 (m) cc_final: 0.8250 (p) REVERT: C 140 ASP cc_start: 0.7777 (m-30) cc_final: 0.7204 (t70) REVERT: C 195 ASP cc_start: 0.7747 (t70) cc_final: 0.7428 (p0) REVERT: C 361 MET cc_start: 0.6871 (mtp) cc_final: 0.6462 (mtp) REVERT: C 401 LEU cc_start: 0.7183 (tp) cc_final: 0.6643 (pp) REVERT: C 427 ASP cc_start: 0.8314 (m-30) cc_final: 0.8102 (t70) REVERT: C 463 MET cc_start: 0.8628 (ttp) cc_final: 0.8197 (ttp) REVERT: C 496 MET cc_start: 0.7627 (ptm) cc_final: 0.7367 (ptm) REVERT: C 519 ASP cc_start: 0.8470 (m-30) cc_final: 0.8095 (m-30) REVERT: C 527 MET cc_start: 0.7063 (mmm) cc_final: 0.6622 (mpp) REVERT: C 607 PHE cc_start: 0.8827 (t80) cc_final: 0.8414 (t80) REVERT: C 610 LEU cc_start: 0.9361 (tt) cc_final: 0.9054 (tp) REVERT: C 619 ASN cc_start: 0.8756 (t0) cc_final: 0.8441 (t0) REVERT: C 668 ASP cc_start: 0.8363 (m-30) cc_final: 0.8122 (m-30) REVERT: C 1178 MET cc_start: 0.8403 (ttp) cc_final: 0.7703 (tmm) REVERT: C 1183 MET cc_start: 0.7902 (mmm) cc_final: 0.7560 (mmm) REVERT: D 46 HIS cc_start: 0.5845 (OUTLIER) cc_final: 0.5608 (t-90) REVERT: D 85 ILE cc_start: 0.8852 (mm) cc_final: 0.8555 (mm) REVERT: D 113 MET cc_start: 0.8476 (mmm) cc_final: 0.8207 (mmm) REVERT: D 185 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7100 (tp30) REVERT: D 228 THR cc_start: 0.8987 (p) cc_final: 0.8553 (t) REVERT: D 380 MET cc_start: 0.7241 (mmm) cc_final: 0.6696 (mmm) REVERT: D 585 MET cc_start: 0.9162 (mmt) cc_final: 0.8390 (mmt) REVERT: D 708 MET cc_start: 0.7358 (pmm) cc_final: 0.6901 (pmm) REVERT: D 791 ASN cc_start: 0.8459 (m110) cc_final: 0.8183 (m110) outliers start: 3 outliers final: 1 residues processed: 478 average time/residue: 0.3455 time to fit residues: 274.8581 Evaluate side-chains 380 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 3.096 ------------------------------------------------------------------------------- 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: 8.9990 chunk 221 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.150275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125993 restraints weight = 52406.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128659 restraints weight = 90427.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129188 restraints weight = 67739.264| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28452 Z= 0.277 Angle : 0.624 9.785 38466 Z= 0.323 Chirality : 0.044 0.213 4270 Planarity : 0.004 0.087 4846 Dihedral : 5.051 29.319 3854 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.07 % Allowed : 0.43 % Favored : 99.50 % 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: -0.57 (0.14), residues: 3504 helix: 0.92 (0.13), residues: 1620 sheet: -2.49 (0.23), residues: 420 loop : -1.14 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 158 HIS 0.005 0.001 HIS D 219 PHE 0.036 0.002 PHE D 584 TYR 0.016 0.002 TYR C 702 ARG 0.004 0.000 ARG C 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6350.14 seconds wall clock time: 116 minutes 19.84 seconds (6979.84 seconds total)