Starting phenix.real_space_refine on Sun Apr 14 08:01:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/04_2024/8ssa_40749_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/04_2024/8ssa_40749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/04_2024/8ssa_40749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/04_2024/8ssa_40749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/04_2024/8ssa_40749_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssa_40749/04_2024/8ssa_40749_updated.pdb" } resolution = 3.88 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= 0.001 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 168 5.16 5 C 20007 2.51 5 N 4985 2.21 5 O 5716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "B GLU 1103": "OE1" <-> "OE2" Residue "D GLU 1103": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30888 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7759 Classifications: {'peptide': 986} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Chain: "B" Number of atoms: 6238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6238 Classifications: {'peptide': 792} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 768} Chain breaks: 1 Chain: "C" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7759 Classifications: {'peptide': 986} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Chain: "D" Number of atoms: 6238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6238 Classifications: {'peptide': 792} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 768} Chain breaks: 1 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PCW': 4} Inner-chain residues flagged as termini: ['pdbres="GLU A1104 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'PCW': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PCW': 4} Inner-chain residues flagged as termini: ['pdbres="GLU C1104 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'PCW': 2, 'SPD': 1} Inner-chain residues flagged as termini: ['pdbres="GLU D1103 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 15.29, per 1000 atoms: 0.50 Number of scatterers: 30888 At special positions: 0 Unit cell: (118.69, 145.25, 194.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 12 15.00 O 5716 8.00 N 4985 7.00 C 20007 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=2.02 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " 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=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " 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=2.02 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: 12.56 Conformation dependent library (CDL) restraints added in 6.1 seconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 28 sheets defined 45.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.588A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.550A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.693A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.554A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.532A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) 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 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.518A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.651A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.856A pdb=" N VAL A 327 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.646A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.698A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.241A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.751A pdb=" N PHE A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 623 removed outlier: 4.039A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 621 " --> pdb=" O THR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.559A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.808A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.826A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.988A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 765 Processing helix chain 'A' and resid 776 through 779 removed outlier: 3.535A pdb=" N GLY A 779 " --> pdb=" O LYS A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 794 through 819 removed outlier: 3.857A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.641A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 851 " --> pdb=" O CYS A 847 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 950 removed outlier: 3.516A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Proline residue: A 930 - end of helix removed outlier: 3.791A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 990 removed outlier: 3.886A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1031 removed outlier: 3.851A pdb=" N ILE A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.718A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.659A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.708A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.836A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.525A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 4.317A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.645A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.572A pdb=" N LEU B 284 " --> pdb=" O TYR B 280 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.946A pdb=" N GLU B 330 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.875A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 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: 3.538A 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 525 through 545 removed outlier: 4.163A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 4.042A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 623 removed outlier: 4.205A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.653A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.636A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.605A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 754 removed outlier: 3.851A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 4.371A pdb=" N LEU B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 751 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 793 through 818 removed outlier: 3.646A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 removed outlier: 3.589A pdb=" N GLY C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.549A pdb=" N ILE C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 removed outlier: 3.692A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.554A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.531A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) 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 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.519A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.652A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.856A pdb=" N VAL C 327 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 335 " --> pdb=" O ALA C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.646A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.697A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 519 Processing helix chain 'C' and resid 523 through 543 removed outlier: 4.240A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 584 removed outlier: 3.751A pdb=" N PHE C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 623 removed outlier: 4.040A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 618 " --> pdb=" O SER C 614 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 removed outlier: 3.560A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 666 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.808A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.827A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 removed outlier: 3.987A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 765 Processing helix chain 'C' and resid 776 through 779 removed outlier: 3.536A pdb=" N GLY C 779 " --> pdb=" O LYS C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 776 through 779' Processing helix chain 'C' and resid 794 through 819 removed outlier: 3.857A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 857 removed outlier: 3.640A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 851 " --> pdb=" O CYS C 847 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 950 removed outlier: 3.516A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) Proline residue: C 930 - end of helix removed outlier: 3.791A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 3.886A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1031 removed outlier: 3.850A pdb=" N ILE C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER C1013 " --> pdb=" O PHE C1009 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.717A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 67 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.659A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.709A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.837A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.525A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 removed outlier: 4.318A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.644A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.572A pdb=" N LEU D 284 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.947A pdb=" N GLU D 330 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 413 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 432 removed outlier: 3.875A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 467 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: 3.539A 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 525 through 545 removed outlier: 4.162A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 4.041A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 623 removed outlier: 4.204A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.653A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.636A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 712 removed outlier: 3.606A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 754 removed outlier: 3.851A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 4.371A pdb=" N LEU D 748 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 751 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 793 through 818 removed outlier: 3.646A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 23 removed outlier: 3.587A pdb=" N THR E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 14 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.668A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 Processing helix chain 'E' and resid 69 through 84 removed outlier: 4.386A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 106 removed outlier: 3.546A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 127 through 157 removed outlier: 3.688A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA E 140 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 23 removed outlier: 3.584A pdb=" N THR F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 14 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 removed outlier: 3.641A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 66 through 84 removed outlier: 4.214A pdb=" N VAL F 69 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.675A pdb=" N SER F 73 " --> pdb=" O PRO F 70 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE F 74 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS F 79 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 83 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 3.646A pdb=" N GLY F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 127 through 157 removed outlier: 3.691A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA F 140 " --> pdb=" O TRP F 136 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 50 Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 132 through 137 removed outlier: 5.839A pdb=" N GLN A 159 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR A 135 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR A 161 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR A 137 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 163 " --> pdb=" O TYR A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 191 through 193 removed outlier: 6.446A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.685A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 395 through 399 removed outlier: 3.772A pdb=" N LYS A 441 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.680A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 357 through 363 removed outlier: 3.805A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 45 through 50 removed outlier: 7.062A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 72 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LEU B 17 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 132 through 137 removed outlier: 5.779A pdb=" N GLN B 159 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR B 135 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR B 161 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR B 137 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 163 " --> pdb=" O TYR B 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 243 through 246 removed outlier: 4.277A pdb=" N GLY B 244 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 361 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.929A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 345 " --> pdb=" O VAL B 338 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 397 through 399 Processing sheet with id= N, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.129A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 42 through 50 Processing sheet with id= P, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= Q, first strand: chain 'C' and resid 132 through 137 removed outlier: 5.839A pdb=" N GLN C 159 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR C 135 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR C 161 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR C 137 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 163 " --> pdb=" O TYR C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 191 through 193 removed outlier: 6.445A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.686A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 395 through 399 removed outlier: 3.771A pdb=" N LYS C 441 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 720 through 722 removed outlier: 3.679A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 357 through 363 removed outlier: 3.805A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 45 through 50 removed outlier: 7.062A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA D 72 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LEU D 17 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 132 through 137 removed outlier: 5.778A pdb=" N GLN D 159 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR D 135 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR D 161 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR D 137 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 163 " --> pdb=" O TYR D 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 243 through 246 removed outlier: 4.278A pdb=" N GLY D 244 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 361 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 337 through 339 removed outlier: 3.929A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 345 " --> pdb=" O VAL D 338 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 397 through 399 Processing sheet with id= AB, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.129A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2928 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: 10.37 Time building geometry restraints manager: 13.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5004 1.31 - 1.44: 8592 1.44 - 1.57: 17645 1.57 - 1.69: 26 1.69 - 1.82: 268 Bond restraints: 31535 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.423 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.416 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.422 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C11 PCW C1103 " pdb=" O3 PCW C1103 " ideal model delta sigma weight residual 1.326 1.415 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C31 PCW D1102 " pdb=" O2 PCW D1102 " ideal model delta sigma weight residual 1.333 1.421 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 31530 not shown) Histogram of bond angle deviations from ideal: 95.65 - 103.74: 312 103.74 - 111.83: 13987 111.83 - 119.92: 14410 119.92 - 128.01: 13545 128.01 - 136.10: 280 Bond angle restraints: 42534 Sorted by residual: angle pdb=" C THR B 383 " pdb=" N GLU B 384 " pdb=" CA GLU B 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" C THR D 383 " pdb=" N GLU D 384 " pdb=" CA GLU D 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" N THR B 383 " pdb=" CA THR B 383 " pdb=" C THR B 383 " ideal model delta sigma weight residual 110.53 102.54 7.99 1.29e+00 6.01e-01 3.84e+01 angle pdb=" N THR D 383 " pdb=" CA THR D 383 " pdb=" C THR D 383 " ideal model delta sigma weight residual 110.53 102.55 7.98 1.29e+00 6.01e-01 3.83e+01 angle pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 ... (remaining 42529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 18350 35.38 - 70.77: 362 70.77 - 106.15: 37 106.15 - 141.53: 6 141.53 - 176.92: 10 Dihedral angle restraints: 18765 sinusoidal: 7683 harmonic: 11082 Sorted by residual: dihedral pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual -180.00 -120.26 -59.74 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER C 403 " pdb=" C SER C 403 " pdb=" N PRO C 404 " pdb=" CA PRO C 404 " ideal model delta harmonic sigma weight residual 180.00 -120.27 -59.73 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER D 403 " pdb=" C SER D 403 " pdb=" N PRO D 404 " pdb=" CA PRO D 404 " ideal model delta harmonic sigma weight residual -180.00 -125.12 -54.88 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 18762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3617 0.070 - 0.140: 931 0.140 - 0.210: 107 0.210 - 0.280: 21 0.280 - 0.350: 6 Chirality restraints: 4682 Sorted by residual: chirality pdb=" CB VAL B 395 " pdb=" CA VAL B 395 " pdb=" CG1 VAL B 395 " pdb=" CG2 VAL B 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB VAL D 395 " pdb=" CA VAL D 395 " pdb=" CG1 VAL D 395 " pdb=" CG2 VAL D 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE D 459 " pdb=" CA ILE D 459 " pdb=" CG1 ILE D 459 " pdb=" CG2 ILE D 459 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 4679 not shown) Planarity restraints: 5306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.089 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO D 717 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " -0.089 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO B 717 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 403 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 404 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.048 5.00e-02 4.00e+02 ... (remaining 5303 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4683 2.75 - 3.29: 30279 3.29 - 3.83: 52617 3.83 - 4.36: 62505 4.36 - 4.90: 101645 Nonbonded interactions: 251729 Sorted by model distance: nonbonded pdb=" OH TYR D 128 " pdb=" OG SER D 243 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR B 128 " pdb=" OG SER B 243 " model vdw 2.213 2.440 nonbonded pdb=" O ASP D 490 " pdb=" OG1 THR D 736 " model vdw 2.239 2.440 nonbonded pdb=" O ASP B 490 " pdb=" OG1 THR B 736 " model vdw 2.240 2.440 nonbonded pdb=" OE2 GLU A 25 " pdb=" OG1 THR A 281 " model vdw 2.267 2.440 ... (remaining 251724 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' and (resid 10 through 821 or resid 1101 through 1103)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.730 Check model and map are aligned: 0.470 Set scattering table: 0.320 Process input model: 80.680 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.220 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 : 0.010 0.105 31535 Z= 0.643 Angle : 1.318 14.561 42534 Z= 0.672 Chirality : 0.062 0.350 4682 Planarity : 0.008 0.135 5306 Dihedral : 14.930 176.918 11647 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.37 % Favored : 87.63 % Rotamer: Outliers : 1.00 % Allowed : 6.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.92 % 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: -5.19 (0.10), residues: 3800 helix: -3.51 (0.07), residues: 1814 sheet: -3.49 (0.23), residues: 342 loop : -3.19 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 130 HIS 0.015 0.004 HIS A 214 PHE 0.037 0.004 PHE C 133 TYR 0.034 0.003 TYR E 149 ARG 0.008 0.001 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 747 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7324 (pt) REVERT: A 137 TYR cc_start: 0.8544 (p90) cc_final: 0.8272 (p90) REVERT: A 440 TYR cc_start: 0.7633 (p90) cc_final: 0.7357 (p90) REVERT: A 518 LEU cc_start: 0.8968 (pp) cc_final: 0.8668 (pp) REVERT: A 814 PHE cc_start: 0.8647 (t80) cc_final: 0.8377 (t80) REVERT: A 906 VAL cc_start: 0.5459 (OUTLIER) cc_final: 0.5185 (p) REVERT: A 1022 VAL cc_start: 0.9150 (m) cc_final: 0.8732 (p) REVERT: B 478 PRO cc_start: 0.5145 (Cg_endo) cc_final: 0.4701 (Cg_exo) REVERT: B 626 VAL cc_start: 0.9569 (t) cc_final: 0.9313 (m) REVERT: B 683 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.6944 (m) REVERT: B 695 LYS cc_start: 0.8469 (mmpt) cc_final: 0.7803 (tptt) REVERT: B 704 LEU cc_start: 0.8622 (pt) cc_final: 0.8081 (pt) REVERT: B 708 MET cc_start: 0.8244 (mtt) cc_final: 0.7935 (ttm) REVERT: B 711 TYR cc_start: 0.8241 (t80) cc_final: 0.7968 (t80) REVERT: C 137 TYR cc_start: 0.8559 (p90) cc_final: 0.8265 (p90) REVERT: C 440 TYR cc_start: 0.7586 (p90) cc_final: 0.7298 (p90) REVERT: C 518 LEU cc_start: 0.9130 (pp) cc_final: 0.8866 (pp) REVERT: C 814 PHE cc_start: 0.8604 (t80) cc_final: 0.8217 (t80) REVERT: C 906 VAL cc_start: 0.5542 (OUTLIER) cc_final: 0.5283 (p) REVERT: C 1022 VAL cc_start: 0.9105 (m) cc_final: 0.8716 (p) REVERT: D 140 ASP cc_start: 0.6617 (t70) cc_final: 0.6282 (t0) REVERT: D 478 PRO cc_start: 0.4901 (Cg_endo) cc_final: 0.4408 (Cg_exo) REVERT: D 503 MET cc_start: 0.7892 (ttm) cc_final: 0.7638 (ttm) REVERT: D 533 TYR cc_start: 0.8497 (t80) cc_final: 0.8270 (t80) REVERT: D 626 VAL cc_start: 0.9464 (t) cc_final: 0.9087 (m) REVERT: D 683 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7414 (m) REVERT: D 704 LEU cc_start: 0.8445 (pt) cc_final: 0.8217 (pt) REVERT: D 807 MET cc_start: 0.7866 (mtp) cc_final: 0.7606 (tmm) REVERT: F 21 ILE cc_start: 0.8384 (pt) cc_final: 0.8118 (mt) outliers start: 33 outliers final: 6 residues processed: 772 average time/residue: 0.3696 time to fit residues: 445.6396 Evaluate side-chains 393 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 382 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 683 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 299 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 112 GLN A 219 HIS A 274 HIS A 318 ASN A 337 GLN A 344 ASN A 747 ASN A 920 ASN B 10 ASN B 46 HIS B 54 ASN B 164 ASN B 214 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 335 GLN B 337 GLN B 344 ASN B 392 GLN B 411 ASN B 461 ASN C 10 ASN C 83 ASN C 112 GLN C 274 HIS C 318 ASN C 337 GLN C 344 ASN C 747 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 ASN C 985 ASN D 10 ASN D 46 HIS D 54 ASN D 159 GLN D 164 ASN ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 ASN D 335 GLN D 337 GLN D 344 ASN D 355 ASN D 392 GLN D 411 ASN D 461 ASN D 587 GLN ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 75 HIS ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS F 107 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31535 Z= 0.226 Angle : 0.722 10.270 42534 Z= 0.377 Chirality : 0.043 0.162 4682 Planarity : 0.006 0.094 5306 Dihedral : 14.653 179.029 4593 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.89 % Favored : 89.66 % Rotamer: Outliers : 3.01 % Allowed : 11.78 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.67 % 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: -3.51 (0.12), residues: 3800 helix: -1.53 (0.11), residues: 1870 sheet: -3.11 (0.23), residues: 378 loop : -3.05 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 460 HIS 0.004 0.001 HIS A 46 PHE 0.039 0.002 PHE A 965 TYR 0.026 0.002 TYR C 980 ARG 0.009 0.001 ARG E 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 480 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8604 (p90) cc_final: 0.8255 (p90) REVERT: A 518 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8526 (pp) REVERT: A 647 TYR cc_start: 0.8001 (p90) cc_final: 0.7754 (p90) REVERT: A 852 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8149 (pt) REVERT: A 938 PHE cc_start: 0.8666 (m-80) cc_final: 0.8370 (m-10) REVERT: A 1022 VAL cc_start: 0.9095 (m) cc_final: 0.8822 (p) REVERT: B 373 TYR cc_start: 0.7286 (p90) cc_final: 0.6951 (p90) REVERT: B 408 MET cc_start: 0.6426 (tmm) cc_final: 0.6087 (tmm) REVERT: B 419 GLU cc_start: 0.7050 (tp30) cc_final: 0.6362 (tm-30) REVERT: B 449 LYS cc_start: 0.6398 (mmtm) cc_final: 0.6143 (mmmt) REVERT: B 527 MET cc_start: 0.7831 (tpp) cc_final: 0.7579 (mtm) REVERT: B 626 VAL cc_start: 0.9585 (t) cc_final: 0.9311 (m) REVERT: B 683 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6509 (m) REVERT: B 695 LYS cc_start: 0.8424 (mmpt) cc_final: 0.7859 (tptt) REVERT: B 711 TYR cc_start: 0.8261 (t80) cc_final: 0.7967 (t80) REVERT: B 788 SER cc_start: 0.8497 (p) cc_final: 0.8270 (p) REVERT: C 71 TYR cc_start: 0.4886 (m-80) cc_final: 0.4260 (m-80) REVERT: C 137 TYR cc_start: 0.8617 (p90) cc_final: 0.8231 (p90) REVERT: C 518 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8711 (pp) REVERT: C 542 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8524 (tp) REVERT: C 647 TYR cc_start: 0.8052 (p90) cc_final: 0.7710 (p90) REVERT: C 814 PHE cc_start: 0.8341 (t80) cc_final: 0.8049 (t80) REVERT: C 852 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8070 (pt) REVERT: C 1000 ASN cc_start: 0.6684 (m-40) cc_final: 0.6159 (m-40) REVERT: C 1022 VAL cc_start: 0.9110 (m) cc_final: 0.8745 (p) REVERT: D 231 ASP cc_start: 0.7623 (t70) cc_final: 0.7419 (p0) REVERT: D 527 MET cc_start: 0.7582 (tpp) cc_final: 0.7376 (mtm) REVERT: D 626 VAL cc_start: 0.9494 (t) cc_final: 0.9155 (m) REVERT: D 669 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9115 (ptpp) REVERT: D 695 LYS cc_start: 0.8427 (mmmt) cc_final: 0.7761 (tptt) REVERT: D 721 MET cc_start: 0.7454 (tpp) cc_final: 0.7213 (tpp) REVERT: D 807 MET cc_start: 0.7823 (mtp) cc_final: 0.7522 (tmm) REVERT: E 123 MET cc_start: 0.4344 (mmm) cc_final: 0.3671 (mmm) REVERT: E 126 ASP cc_start: 0.6857 (p0) cc_final: 0.6654 (p0) REVERT: E 144 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6380 (tt) REVERT: F 123 MET cc_start: 0.3912 (mmm) cc_final: 0.3476 (mmm) outliers start: 99 outliers final: 42 residues processed: 553 average time/residue: 0.4290 time to fit residues: 381.2751 Evaluate side-chains 414 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 364 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 236 optimal weight: 0.0870 chunk 95 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 344 optimal weight: 7.9990 chunk 118 optimal weight: 0.0050 chunk 278 optimal weight: 10.0000 overall best weight: 2.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 246 GLN B 355 ASN B 587 GLN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31535 Z= 0.273 Angle : 0.713 15.339 42534 Z= 0.367 Chirality : 0.044 0.306 4682 Planarity : 0.005 0.084 5306 Dihedral : 13.991 179.746 4587 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.03 % Favored : 88.61 % Rotamer: Outliers : 3.50 % Allowed : 14.39 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.65 % 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: -2.66 (0.13), residues: 3800 helix: -0.62 (0.12), residues: 1862 sheet: -2.81 (0.24), residues: 408 loop : -2.88 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 460 HIS 0.021 0.002 HIS C 274 PHE 0.038 0.002 PHE C 965 TYR 0.026 0.002 TYR C 980 ARG 0.006 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 395 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7551 (tm) REVERT: A 518 LEU cc_start: 0.9079 (pp) cc_final: 0.8724 (pp) REVERT: A 852 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8150 (pt) REVERT: A 886 LEU cc_start: 0.8646 (mt) cc_final: 0.8384 (pt) REVERT: A 999 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: A 1022 VAL cc_start: 0.9032 (m) cc_final: 0.8768 (p) REVERT: B 246 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5633 (tt0) REVERT: B 373 TYR cc_start: 0.7440 (p90) cc_final: 0.7163 (p90) REVERT: B 419 GLU cc_start: 0.6893 (tp30) cc_final: 0.6395 (tm-30) REVERT: B 449 LYS cc_start: 0.6225 (mmtm) cc_final: 0.6006 (mmmt) REVERT: B 527 MET cc_start: 0.7919 (tpp) cc_final: 0.7643 (mtm) REVERT: B 626 VAL cc_start: 0.9557 (t) cc_final: 0.9267 (m) REVERT: B 695 LYS cc_start: 0.8456 (mmpt) cc_final: 0.7963 (tptt) REVERT: B 702 TYR cc_start: 0.8517 (t80) cc_final: 0.8113 (t80) REVERT: B 711 TYR cc_start: 0.8432 (t80) cc_final: 0.8048 (t80) REVERT: B 789 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8731 (tt) REVERT: C 71 TYR cc_start: 0.5029 (m-80) cc_final: 0.4524 (m-80) REVERT: C 137 TYR cc_start: 0.8670 (p90) cc_final: 0.8305 (p90) REVERT: C 382 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7492 (tm) REVERT: C 518 LEU cc_start: 0.9182 (pp) cc_final: 0.8860 (pp) REVERT: C 647 TYR cc_start: 0.8105 (p90) cc_final: 0.7898 (p90) REVERT: C 814 PHE cc_start: 0.8285 (t80) cc_final: 0.8009 (t80) REVERT: C 852 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8098 (pt) REVERT: C 999 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6060 (m-80) REVERT: C 1022 VAL cc_start: 0.9073 (m) cc_final: 0.8727 (p) REVERT: D 18 PHE cc_start: 0.8069 (m-80) cc_final: 0.7863 (m-10) REVERT: D 111 ILE cc_start: 0.8111 (mp) cc_final: 0.7875 (mm) REVERT: D 231 ASP cc_start: 0.7769 (t0) cc_final: 0.7490 (p0) REVERT: D 419 GLU cc_start: 0.6729 (tp30) cc_final: 0.6232 (tm-30) REVERT: D 527 MET cc_start: 0.7813 (tpp) cc_final: 0.7586 (mtm) REVERT: D 626 VAL cc_start: 0.9438 (t) cc_final: 0.9205 (m) REVERT: D 695 LYS cc_start: 0.8466 (mmmt) cc_final: 0.7993 (tptt) REVERT: D 789 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8742 (tt) REVERT: D 807 MET cc_start: 0.7854 (mtp) cc_final: 0.7462 (tmm) REVERT: E 123 MET cc_start: 0.4473 (mmm) cc_final: 0.3841 (mmm) REVERT: E 126 ASP cc_start: 0.6991 (p0) cc_final: 0.6776 (p0) REVERT: E 144 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6368 (tt) REVERT: F 123 MET cc_start: 0.4107 (mmm) cc_final: 0.3714 (mmm) outliers start: 115 outliers final: 65 residues processed: 482 average time/residue: 0.4041 time to fit residues: 323.3945 Evaluate side-chains 419 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 344 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 348 optimal weight: 0.3980 chunk 369 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 330 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31535 Z= 0.235 Angle : 0.670 13.680 42534 Z= 0.344 Chirality : 0.043 0.266 4682 Planarity : 0.005 0.077 5306 Dihedral : 13.536 179.911 4585 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.29 % Favored : 89.45 % Rotamer: Outliers : 3.96 % Allowed : 15.22 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.51 % 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: -2.10 (0.13), residues: 3800 helix: -0.05 (0.12), residues: 1840 sheet: -2.57 (0.25), residues: 386 loop : -2.72 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 460 HIS 0.004 0.001 HIS A 46 PHE 0.031 0.002 PHE C 965 TYR 0.031 0.002 TYR D 673 ARG 0.006 0.001 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 383 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7879 (tppt) REVERT: A 382 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7561 (tm) REVERT: A 518 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 541 PHE cc_start: 0.7731 (t80) cc_final: 0.7524 (t80) REVERT: A 852 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8052 (pt) REVERT: A 999 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: A 1000 ASN cc_start: 0.6535 (t0) cc_final: 0.6147 (t0) REVERT: B 113 MET cc_start: 0.7918 (mpp) cc_final: 0.7205 (mtm) REVERT: B 373 TYR cc_start: 0.7596 (p90) cc_final: 0.7214 (p90) REVERT: B 398 THR cc_start: 0.4751 (OUTLIER) cc_final: 0.4536 (m) REVERT: B 419 GLU cc_start: 0.7044 (tp30) cc_final: 0.6670 (tm-30) REVERT: B 449 LYS cc_start: 0.6195 (mmtm) cc_final: 0.5853 (tmtt) REVERT: B 476 ILE cc_start: 0.4516 (OUTLIER) cc_final: 0.4157 (pt) REVERT: B 527 MET cc_start: 0.7846 (tpp) cc_final: 0.7624 (mtm) REVERT: B 695 LYS cc_start: 0.8418 (mmpt) cc_final: 0.7968 (tptp) REVERT: B 789 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8730 (tt) REVERT: C 71 TYR cc_start: 0.4999 (m-80) cc_final: 0.4662 (m-80) REVERT: C 379 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7813 (tppt) REVERT: C 382 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7572 (tm) REVERT: C 518 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8772 (pp) REVERT: C 647 TYR cc_start: 0.8196 (p90) cc_final: 0.7986 (p90) REVERT: C 852 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7929 (pt) REVERT: C 1022 VAL cc_start: 0.8957 (m) cc_final: 0.8727 (p) REVERT: D 18 PHE cc_start: 0.7960 (m-80) cc_final: 0.7758 (m-10) REVERT: D 111 ILE cc_start: 0.8104 (mp) cc_final: 0.7876 (mm) REVERT: D 231 ASP cc_start: 0.7711 (t0) cc_final: 0.7459 (p0) REVERT: D 449 LYS cc_start: 0.6243 (mmtm) cc_final: 0.5606 (tmtt) REVERT: D 476 ILE cc_start: 0.4610 (OUTLIER) cc_final: 0.4315 (pt) REVERT: D 626 VAL cc_start: 0.9423 (t) cc_final: 0.9208 (m) REVERT: D 669 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9058 (ptpp) REVERT: D 695 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8001 (tptt) REVERT: D 789 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8674 (tt) REVERT: D 807 MET cc_start: 0.7787 (mtp) cc_final: 0.7417 (tmm) REVERT: E 123 MET cc_start: 0.4571 (mmm) cc_final: 0.3951 (mmm) REVERT: F 123 MET cc_start: 0.4188 (mmm) cc_final: 0.3607 (mmm) outliers start: 130 outliers final: 70 residues processed: 479 average time/residue: 0.3991 time to fit residues: 319.0307 Evaluate side-chains 428 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 343 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 274 HIS ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 274 HIS C 274 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31535 Z= 0.390 Angle : 0.757 13.633 42534 Z= 0.388 Chirality : 0.046 0.234 4682 Planarity : 0.005 0.076 5306 Dihedral : 13.607 172.805 4583 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.05 % Favored : 87.68 % Rotamer: Outliers : 3.96 % Allowed : 16.56 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.46 % 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: -2.09 (0.14), residues: 3800 helix: -0.04 (0.12), residues: 1836 sheet: -2.53 (0.26), residues: 382 loop : -2.73 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 887 HIS 0.012 0.002 HIS A 274 PHE 0.023 0.002 PHE C 965 TYR 0.030 0.002 TYR A 980 ARG 0.005 0.001 ARG A 991 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 361 time to evaluate : 3.740 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 71 TYR cc_start: 0.5215 (m-80) cc_final: 0.4484 (m-10) REVERT: A 137 TYR cc_start: 0.8726 (p90) cc_final: 0.8396 (p90) REVERT: A 382 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7600 (tm) REVERT: A 518 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8839 (pp) REVERT: A 852 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8435 (pt) REVERT: A 1000 ASN cc_start: 0.6666 (t0) cc_final: 0.6282 (t0) REVERT: B 408 MET cc_start: 0.6294 (tmm) cc_final: 0.6067 (tmm) REVERT: B 419 GLU cc_start: 0.6969 (tp30) cc_final: 0.6559 (tm-30) REVERT: B 476 ILE cc_start: 0.4325 (OUTLIER) cc_final: 0.4002 (pt) REVERT: B 695 LYS cc_start: 0.8431 (mmpt) cc_final: 0.7971 (tptp) REVERT: B 732 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: B 789 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8981 (tt) REVERT: C 71 TYR cc_start: 0.5237 (m-80) cc_final: 0.4822 (m-80) REVERT: C 137 TYR cc_start: 0.8710 (p90) cc_final: 0.8493 (p90) REVERT: C 382 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7687 (tm) REVERT: C 466 GLU cc_start: 0.7976 (tt0) cc_final: 0.7754 (tt0) REVERT: C 518 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8968 (pp) REVERT: C 852 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8221 (pt) REVERT: C 999 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: D 18 PHE cc_start: 0.8237 (m-80) cc_final: 0.8020 (m-10) REVERT: D 231 ASP cc_start: 0.7831 (t0) cc_final: 0.7513 (p0) REVERT: D 789 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8988 (tt) REVERT: D 807 MET cc_start: 0.7865 (mtp) cc_final: 0.7532 (tmm) REVERT: E 123 MET cc_start: 0.4685 (mmm) cc_final: 0.4167 (mmm) REVERT: E 146 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8365 (t80) REVERT: F 123 MET cc_start: 0.4495 (mmm) cc_final: 0.4214 (mmm) outliers start: 130 outliers final: 84 residues processed: 460 average time/residue: 0.3873 time to fit residues: 301.1484 Evaluate side-chains 420 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 324 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 146 PHE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 30.0000 chunk 332 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 369 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN C 236 GLN C 274 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31535 Z= 0.263 Angle : 0.688 13.518 42534 Z= 0.351 Chirality : 0.044 0.271 4682 Planarity : 0.005 0.073 5306 Dihedral : 13.163 169.732 4583 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.50 % Favored : 89.29 % Rotamer: Outliers : 3.77 % Allowed : 17.56 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3800 helix: 0.23 (0.12), residues: 1834 sheet: -2.50 (0.24), residues: 398 loop : -2.72 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 323 HIS 0.008 0.001 HIS A 412 PHE 0.022 0.002 PHE C 965 TYR 0.028 0.002 TYR C 980 ARG 0.006 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 351 time to evaluate : 3.772 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 71 TYR cc_start: 0.5245 (m-80) cc_final: 0.4560 (m-10) REVERT: A 137 TYR cc_start: 0.8697 (p90) cc_final: 0.8320 (p90) REVERT: A 323 TRP cc_start: 0.5690 (OUTLIER) cc_final: 0.5064 (p-90) REVERT: A 382 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7536 (tm) REVERT: A 456 ASP cc_start: 0.8213 (p0) cc_final: 0.7924 (p0) REVERT: A 518 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8726 (pp) REVERT: B 527 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (mtm) REVERT: B 695 LYS cc_start: 0.8421 (mmpt) cc_final: 0.7988 (tptp) REVERT: B 789 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8780 (tt) REVERT: C 137 TYR cc_start: 0.8687 (p90) cc_final: 0.8399 (p90) REVERT: C 190 ARG cc_start: 0.6844 (tpt170) cc_final: 0.6480 (tpp-160) REVERT: C 382 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7626 (tm) REVERT: C 466 GLU cc_start: 0.8024 (tt0) cc_final: 0.7757 (tt0) REVERT: C 518 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8847 (pp) REVERT: C 852 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8200 (pt) REVERT: C 999 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6167 (m-80) REVERT: D 18 PHE cc_start: 0.8141 (m-80) cc_final: 0.7929 (m-10) REVERT: D 231 ASP cc_start: 0.7738 (t0) cc_final: 0.7480 (p0) REVERT: D 474 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6320 (mt) REVERT: D 496 MET cc_start: 0.7237 (ppp) cc_final: 0.6960 (ppp) REVERT: D 673 TYR cc_start: 0.7797 (m-80) cc_final: 0.7458 (m-80) REVERT: D 682 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: D 695 LYS cc_start: 0.8590 (mmmt) cc_final: 0.7964 (tptt) REVERT: D 789 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8802 (tt) REVERT: D 807 MET cc_start: 0.7756 (mtp) cc_final: 0.7437 (tmm) REVERT: E 123 MET cc_start: 0.4653 (mmm) cc_final: 0.4179 (mmm) REVERT: F 123 MET cc_start: 0.4403 (mmm) cc_final: 0.4140 (mmm) outliers start: 124 outliers final: 78 residues processed: 444 average time/residue: 0.3952 time to fit residues: 295.8548 Evaluate side-chains 402 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 312 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 951 ILE Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 682 PHE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 210 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 311 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 368 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS A 435 HIS B 214 HIS B 355 ASN C 236 GLN C 274 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31535 Z= 0.173 Angle : 0.648 13.633 42534 Z= 0.330 Chirality : 0.042 0.241 4682 Planarity : 0.004 0.072 5306 Dihedral : 12.577 170.166 4583 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.53 % Favored : 90.26 % Rotamer: Outliers : 2.74 % Allowed : 19.20 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.30 % 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: -1.59 (0.14), residues: 3800 helix: 0.51 (0.13), residues: 1822 sheet: -2.42 (0.25), residues: 380 loop : -2.62 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 887 HIS 0.017 0.001 HIS A 274 PHE 0.022 0.001 PHE E 146 TYR 0.032 0.001 TYR C 980 ARG 0.004 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 378 time to evaluate : 3.429 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 71 TYR cc_start: 0.5087 (m-80) cc_final: 0.4224 (m-10) REVERT: A 137 TYR cc_start: 0.8677 (p90) cc_final: 0.8284 (p90) REVERT: A 382 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7552 (tm) REVERT: A 456 ASP cc_start: 0.8084 (p0) cc_final: 0.7750 (p0) REVERT: A 498 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7987 (tp) REVERT: A 518 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8630 (pp) REVERT: A 674 MET cc_start: 0.8276 (mtp) cc_final: 0.7857 (mtp) REVERT: A 879 LYS cc_start: 0.7554 (ttpt) cc_final: 0.7242 (tttm) REVERT: B 503 MET cc_start: 0.8083 (tpp) cc_final: 0.7707 (tpp) REVERT: B 668 ASP cc_start: 0.8929 (t70) cc_final: 0.8717 (m-30) REVERT: B 695 LYS cc_start: 0.8418 (mmpt) cc_final: 0.8039 (tptp) REVERT: B 732 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6461 (m-80) REVERT: B 789 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8582 (tt) REVERT: C 137 TYR cc_start: 0.8655 (p90) cc_final: 0.8252 (p90) REVERT: C 382 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7569 (tm) REVERT: C 469 TYR cc_start: 0.6822 (t80) cc_final: 0.6331 (t80) REVERT: C 498 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8066 (tp) REVERT: C 518 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8726 (pp) REVERT: C 585 MET cc_start: 0.8470 (mpt) cc_final: 0.8152 (mmt) REVERT: C 669 LYS cc_start: 0.8705 (tppt) cc_final: 0.8409 (tppt) REVERT: C 852 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8236 (pt) REVERT: C 999 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6083 (m-80) REVERT: D 111 ILE cc_start: 0.8075 (mp) cc_final: 0.7814 (mm) REVERT: D 442 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7410 (pp) REVERT: D 503 MET cc_start: 0.8173 (tpt) cc_final: 0.7912 (tpt) REVERT: D 673 TYR cc_start: 0.7624 (m-80) cc_final: 0.7292 (m-80) REVERT: D 695 LYS cc_start: 0.8522 (mmmt) cc_final: 0.7939 (tptt) REVERT: D 732 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: D 789 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8528 (tt) REVERT: D 807 MET cc_start: 0.7618 (mtp) cc_final: 0.7312 (tmm) REVERT: E 123 MET cc_start: 0.4724 (mmm) cc_final: 0.4247 (mmm) REVERT: F 123 MET cc_start: 0.4280 (mmm) cc_final: 0.3923 (mmm) outliers start: 90 outliers final: 56 residues processed: 443 average time/residue: 0.3933 time to fit residues: 294.1257 Evaluate side-chains 400 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 331 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 951 ILE Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 732 TYR Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 0.0670 chunk 147 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 250 optimal weight: 0.4980 chunk 182 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 289 optimal weight: 0.4980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS C 274 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN D 355 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 31535 Z= 0.167 Angle : 0.656 13.286 42534 Z= 0.328 Chirality : 0.042 0.258 4682 Planarity : 0.004 0.071 5306 Dihedral : 12.179 171.482 4583 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.89 % Favored : 90.92 % Rotamer: Outliers : 2.47 % Allowed : 19.96 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3800 helix: 0.66 (0.13), residues: 1824 sheet: -2.29 (0.25), residues: 380 loop : -2.60 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 460 HIS 0.018 0.001 HIS A 274 PHE 0.020 0.001 PHE E 146 TYR 0.030 0.001 TYR C 980 ARG 0.005 0.000 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 389 time to evaluate : 3.678 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: A 71 TYR cc_start: 0.5098 (m-80) cc_final: 0.4294 (m-80) REVERT: A 137 TYR cc_start: 0.8659 (p90) cc_final: 0.8109 (p90) REVERT: A 363 LEU cc_start: 0.7766 (tp) cc_final: 0.7390 (tp) REVERT: A 382 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7535 (tm) REVERT: A 498 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8002 (tp) REVERT: A 518 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8561 (pp) REVERT: A 585 MET cc_start: 0.8346 (mpt) cc_final: 0.8125 (mmt) REVERT: A 669 LYS cc_start: 0.8711 (tppt) cc_final: 0.8440 (tppt) REVERT: A 886 LEU cc_start: 0.8431 (pt) cc_final: 0.7526 (mt) REVERT: A 938 PHE cc_start: 0.8407 (m-80) cc_final: 0.7885 (t80) REVERT: A 968 LEU cc_start: 0.9516 (mt) cc_final: 0.9170 (mt) REVERT: B 503 MET cc_start: 0.8107 (tpp) cc_final: 0.7598 (tpp) REVERT: B 668 ASP cc_start: 0.8942 (t70) cc_final: 0.8740 (m-30) REVERT: B 695 LYS cc_start: 0.8268 (mmpt) cc_final: 0.7969 (tptt) REVERT: B 732 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6331 (m-80) REVERT: B 767 TRP cc_start: 0.7862 (m-90) cc_final: 0.6052 (m-90) REVERT: B 788 SER cc_start: 0.8572 (p) cc_final: 0.8254 (m) REVERT: B 789 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8478 (tt) REVERT: C 137 TYR cc_start: 0.8693 (p90) cc_final: 0.8221 (p90) REVERT: C 363 LEU cc_start: 0.7838 (tp) cc_final: 0.7477 (tp) REVERT: C 382 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7494 (tm) REVERT: C 511 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7716 (tptp) REVERT: C 518 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8687 (pp) REVERT: C 585 MET cc_start: 0.8370 (mpt) cc_final: 0.8133 (mmt) REVERT: C 669 LYS cc_start: 0.8653 (tppt) cc_final: 0.8359 (tppt) REVERT: C 814 PHE cc_start: 0.8228 (t80) cc_final: 0.8001 (t80) REVERT: C 879 LYS cc_start: 0.7204 (ttpt) cc_final: 0.6945 (ttpt) REVERT: C 886 LEU cc_start: 0.8521 (pt) cc_final: 0.7608 (mt) REVERT: C 999 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.5980 (m-80) REVERT: D 111 ILE cc_start: 0.7942 (mp) cc_final: 0.7661 (mm) REVERT: D 138 ASP cc_start: 0.6505 (t0) cc_final: 0.6162 (t0) REVERT: D 140 ASP cc_start: 0.6436 (t0) cc_final: 0.6096 (t0) REVERT: D 442 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7495 (pp) REVERT: D 479 LEU cc_start: 0.7915 (mt) cc_final: 0.7208 (mp) REVERT: D 673 TYR cc_start: 0.7566 (m-80) cc_final: 0.7163 (m-80) REVERT: D 695 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8002 (tptt) REVERT: D 732 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6585 (m-80) REVERT: D 789 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8435 (tt) REVERT: E 123 MET cc_start: 0.4669 (mmm) cc_final: 0.4213 (mmm) REVERT: F 123 MET cc_start: 0.4080 (mmm) cc_final: 0.3801 (mmm) REVERT: F 143 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7690 (mm) outliers start: 81 outliers final: 56 residues processed: 443 average time/residue: 0.3887 time to fit residues: 289.1256 Evaluate side-chains 402 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 334 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 951 ILE Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 732 TYR Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 0.8980 chunk 352 optimal weight: 0.9990 chunk 321 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 324 optimal weight: 5.9990 chunk 341 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31535 Z= 0.184 Angle : 0.671 17.101 42534 Z= 0.334 Chirality : 0.043 0.275 4682 Planarity : 0.004 0.068 5306 Dihedral : 11.992 167.992 4583 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.58 % Favored : 90.18 % Rotamer: Outliers : 2.34 % Allowed : 20.60 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.32 % 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: -1.33 (0.14), residues: 3800 helix: 0.73 (0.13), residues: 1834 sheet: -2.20 (0.26), residues: 356 loop : -2.54 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 460 HIS 0.011 0.001 HIS A 274 PHE 0.020 0.001 PHE E 146 TYR 0.029 0.001 TYR A 980 ARG 0.005 0.000 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 346 time to evaluate : 3.750 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: A 71 TYR cc_start: 0.5071 (m-80) cc_final: 0.4325 (m-80) REVERT: A 137 TYR cc_start: 0.8681 (p90) cc_final: 0.8171 (p90) REVERT: A 363 LEU cc_start: 0.7856 (tp) cc_final: 0.7507 (tp) REVERT: A 382 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7543 (tm) REVERT: A 408 MET cc_start: 0.7377 (tpp) cc_final: 0.6431 (ttt) REVERT: A 498 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8130 (tp) REVERT: A 518 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8621 (pp) REVERT: A 669 LYS cc_start: 0.8705 (tppt) cc_final: 0.8456 (tppt) REVERT: A 814 PHE cc_start: 0.8421 (t80) cc_final: 0.8099 (t80) REVERT: A 886 LEU cc_start: 0.8480 (pt) cc_final: 0.7557 (mt) REVERT: A 938 PHE cc_start: 0.8379 (m-80) cc_final: 0.7901 (t80) REVERT: A 968 LEU cc_start: 0.9522 (mt) cc_final: 0.9143 (mt) REVERT: B 503 MET cc_start: 0.8137 (tpp) cc_final: 0.7610 (tpp) REVERT: B 695 LYS cc_start: 0.8252 (mmpt) cc_final: 0.8029 (tptp) REVERT: B 732 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: B 788 SER cc_start: 0.8528 (p) cc_final: 0.8251 (m) REVERT: B 789 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8491 (tt) REVERT: C 137 TYR cc_start: 0.8688 (p90) cc_final: 0.8154 (p90) REVERT: C 363 LEU cc_start: 0.7857 (tp) cc_final: 0.7490 (tp) REVERT: C 382 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7524 (tm) REVERT: C 408 MET cc_start: 0.7597 (tpp) cc_final: 0.6525 (ttt) REVERT: C 511 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7685 (tptp) REVERT: C 518 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8739 (pp) REVERT: C 585 MET cc_start: 0.8466 (mpt) cc_final: 0.8161 (mmt) REVERT: C 669 LYS cc_start: 0.8692 (tppt) cc_final: 0.8402 (tppt) REVERT: C 814 PHE cc_start: 0.8247 (t80) cc_final: 0.8023 (t80) REVERT: C 849 LEU cc_start: 0.8183 (mm) cc_final: 0.7897 (mt) REVERT: C 879 LYS cc_start: 0.7120 (ttpt) cc_final: 0.6902 (tttm) REVERT: C 886 LEU cc_start: 0.8516 (pt) cc_final: 0.7547 (mt) REVERT: C 999 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: D 111 ILE cc_start: 0.7886 (mp) cc_final: 0.7656 (mm) REVERT: D 138 ASP cc_start: 0.6678 (t0) cc_final: 0.6310 (t0) REVERT: D 140 ASP cc_start: 0.6373 (t0) cc_final: 0.6092 (t0) REVERT: D 442 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7568 (pp) REVERT: D 673 TYR cc_start: 0.7595 (m-80) cc_final: 0.7214 (m-80) REVERT: D 695 LYS cc_start: 0.8516 (mmmt) cc_final: 0.7996 (tptt) REVERT: D 732 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: D 788 SER cc_start: 0.8507 (p) cc_final: 0.8297 (m) REVERT: D 789 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8424 (tt) REVERT: E 123 MET cc_start: 0.4699 (mmm) cc_final: 0.4282 (mmm) REVERT: E 143 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7701 (mp) REVERT: F 123 MET cc_start: 0.3984 (mmm) cc_final: 0.3720 (mmm) REVERT: F 143 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7668 (mm) outliers start: 77 outliers final: 52 residues processed: 399 average time/residue: 0.3777 time to fit residues: 255.0251 Evaluate side-chains 391 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 326 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 951 ILE Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 732 TYR Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 0.5980 chunk 362 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 350 optimal weight: 0.0870 chunk 303 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31535 Z= 0.234 Angle : 0.695 14.705 42534 Z= 0.348 Chirality : 0.044 0.234 4682 Planarity : 0.004 0.066 5306 Dihedral : 11.983 162.672 4583 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.24 % Favored : 89.58 % Rotamer: Outliers : 2.43 % Allowed : 20.57 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.88 % Twisted General : 0.38 % 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: -1.33 (0.14), residues: 3800 helix: 0.73 (0.13), residues: 1828 sheet: -2.29 (0.26), residues: 342 loop : -2.51 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 767 HIS 0.015 0.001 HIS A 274 PHE 0.025 0.002 PHE A1007 TYR 0.035 0.002 TYR A 980 ARG 0.005 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 329 time to evaluate : 3.492 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: A 71 TYR cc_start: 0.5113 (m-80) cc_final: 0.4354 (m-80) REVERT: A 137 TYR cc_start: 0.8720 (p90) cc_final: 0.8292 (p90) REVERT: A 382 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7608 (tm) REVERT: A 408 MET cc_start: 0.7545 (tpp) cc_final: 0.6680 (ttt) REVERT: A 518 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 669 LYS cc_start: 0.8731 (tppt) cc_final: 0.8489 (tppt) REVERT: A 814 PHE cc_start: 0.8443 (t80) cc_final: 0.8092 (t80) REVERT: A 886 LEU cc_start: 0.8494 (pt) cc_final: 0.7565 (mt) REVERT: B 138 ASP cc_start: 0.7722 (t0) cc_final: 0.7138 (t0) REVERT: B 503 MET cc_start: 0.8123 (tpp) cc_final: 0.7556 (tpp) REVERT: B 629 MET cc_start: 0.8243 (tpp) cc_final: 0.7508 (mtt) REVERT: B 695 LYS cc_start: 0.8242 (mmpt) cc_final: 0.7990 (tptt) REVERT: B 732 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: B 788 SER cc_start: 0.8550 (p) cc_final: 0.8256 (m) REVERT: B 789 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8602 (tt) REVERT: C 137 TYR cc_start: 0.8706 (p90) cc_final: 0.8277 (p90) REVERT: C 382 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7558 (tm) REVERT: C 408 MET cc_start: 0.7620 (tpp) cc_final: 0.6730 (ttt) REVERT: C 511 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7701 (tptp) REVERT: C 518 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8817 (pp) REVERT: C 669 LYS cc_start: 0.8724 (tppt) cc_final: 0.8459 (tppt) REVERT: C 849 LEU cc_start: 0.8167 (mm) cc_final: 0.7858 (mt) REVERT: C 879 LYS cc_start: 0.7126 (ttpt) cc_final: 0.6911 (tttm) REVERT: C 999 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5962 (m-80) REVERT: D 111 ILE cc_start: 0.7946 (mp) cc_final: 0.7736 (mm) REVERT: D 138 ASP cc_start: 0.6819 (t0) cc_final: 0.6338 (t0) REVERT: D 140 ASP cc_start: 0.6372 (t0) cc_final: 0.5908 (t0) REVERT: D 408 MET cc_start: 0.5932 (tmm) cc_final: 0.5028 (tmm) REVERT: D 442 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7622 (pp) REVERT: D 673 TYR cc_start: 0.7881 (m-80) cc_final: 0.7577 (m-80) REVERT: D 695 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8020 (tptt) REVERT: D 732 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: D 789 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8672 (tt) REVERT: E 123 MET cc_start: 0.4695 (mmm) cc_final: 0.4355 (mmm) REVERT: F 123 MET cc_start: 0.4046 (mmm) cc_final: 0.3816 (mmm) REVERT: F 143 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7667 (mm) outliers start: 80 outliers final: 59 residues processed: 390 average time/residue: 0.3822 time to fit residues: 252.3981 Evaluate side-chains 381 residues out of total 3286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 311 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 951 ILE Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 732 TYR Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 44 optimal weight: 0.0020 chunk 84 optimal weight: 3.9990 chunk 303 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 311 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.152563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.128456 restraints weight = 75498.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.127343 restraints weight = 82857.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.125339 restraints weight = 64767.759| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31535 Z= 0.229 Angle : 0.688 14.640 42534 Z= 0.343 Chirality : 0.044 0.229 4682 Planarity : 0.004 0.061 5306 Dihedral : 11.889 162.064 4583 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.13 % Favored : 89.66 % Rotamer: Outliers : 2.40 % Allowed : 20.88 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.88 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3800 helix: 0.73 (0.13), residues: 1838 sheet: -2.20 (0.26), residues: 344 loop : -2.50 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 887 HIS 0.011 0.001 HIS A 274 PHE 0.021 0.002 PHE E 146 TYR 0.035 0.001 TYR A 980 ARG 0.005 0.000 ARG E 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6497.57 seconds wall clock time: 124 minutes 20.23 seconds (7460.23 seconds total)