Starting phenix.real_space_refine on Tue Mar 19 17:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/03_2024/7wae_32383_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/03_2024/7wae_32383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/03_2024/7wae_32383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/03_2024/7wae_32383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/03_2024/7wae_32383_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/03_2024/7wae_32383_updated.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 11 5.21 5 S 88 5.16 5 C 15578 2.51 5 N 4357 2.21 5 O 4792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 529": "OE1" <-> "OE2" Residue "C GLU 533": "OE1" <-> "OE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24850 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 877, 6683 Classifications: {'peptide': 877} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 841} Chain: "B" Number of atoms: 6683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 877, 6683 Classifications: {'peptide': 877} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 841} Chain: "C" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5510 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 695} Chain: "D" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5510 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 695} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Time building chain proxies: 13.20, per 1000 atoms: 0.53 Number of scatterers: 24850 At special positions: 0 Unit cell: (165.17, 164.34, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 24 15.00 Mg 11 11.99 O 4792 8.00 N 4357 7.00 C 15578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.39 Conformation dependent library (CDL) restraints added in 4.3 seconds 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 26 sheets defined 36.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.72 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 119 through 139 removed outlier: 3.863A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.876A pdb=" N GLN A 247 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 253 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.618A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 410 through 423 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.192A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 595 through 607 removed outlier: 3.831A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.585A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.676A pdb=" N GLN A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 720 Processing helix chain 'A' and resid 750 through 762 removed outlier: 3.575A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 842 through 851 Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 119 through 139 removed outlier: 3.827A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.997A pdb=" N GLN B 247 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 248 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 253 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.520A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.206A pdb=" N LEU B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 546 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 595 through 607 removed outlier: 3.786A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 628 removed outlier: 3.622A pdb=" N MET B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 691 through 707 removed outlier: 3.644A pdb=" N GLN B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.610A pdb=" N PHE B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 792 Processing helix chain 'B' and resid 811 through 825 Processing helix chain 'B' and resid 842 through 851 Processing helix chain 'B' and resid 866 through 875 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 77 through 91 Processing helix chain 'C' and resid 119 through 139 removed outlier: 3.809A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 243 through 253 removed outlier: 4.564A pdb=" N GLN C 247 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 248 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 291 Processing helix chain 'C' and resid 336 through 344 removed outlier: 4.704A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 499 through 512 Processing helix chain 'C' and resid 540 through 547 removed outlier: 4.128A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 595 through 607 removed outlier: 3.780A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 628 removed outlier: 3.689A pdb=" N MET C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA C 628 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 683 through 685 No H-bonds generated for 'chain 'C' and resid 683 through 685' Processing helix chain 'C' and resid 691 through 707 removed outlier: 3.652A pdb=" N GLN C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 720 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.790A pdb=" N GLU D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 119 through 139 removed outlier: 3.780A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 229 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.644A pdb=" N VAL D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 291 Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.679A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 410 through 423 Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 499 through 512 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.211A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 607 removed outlier: 3.773A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 628 removed outlier: 3.654A pdb=" N MET D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA D 628 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 Processing helix chain 'D' and resid 683 through 685 No H-bonds generated for 'chain 'D' and resid 683 through 685' Processing helix chain 'D' and resid 691 through 707 removed outlier: 3.655A pdb=" N GLN D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 720 Processing sheet with id= A, first strand: chain 'A' and resid 99 through 103 removed outlier: 3.804A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.784A pdb=" N LEU A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 320 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG A 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU A 322 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP A 307 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 450 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= F, first strand: chain 'A' and resid 673 through 677 removed outlier: 6.591A pdb=" N ILE A 665 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE A 527 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 733 through 736 removed outlier: 3.514A pdb=" N ASN A 733 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A 795 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 771 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 797 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 835 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE A 798 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU A 837 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 99 through 103 removed outlier: 3.749A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= J, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= K, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.812A pdb=" N LEU B 311 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 320 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU B 322 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASP B 307 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 450 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= M, first strand: chain 'B' and resid 673 through 677 removed outlier: 6.588A pdb=" N ILE B 665 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE B 527 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.626A pdb=" N ASN B 733 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 744 " --> pdb=" O ASN B 733 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU B 795 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL B 771 " --> pdb=" O GLU B 795 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 797 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 835 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE B 798 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU B 837 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.807A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.575A pdb=" N VAL C 297 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 400 through 403 removed outlier: 6.848A pdb=" N LEU C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL C 320 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG C 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU C 322 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP C 307 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 450 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= T, first strand: chain 'C' and resid 673 through 677 removed outlier: 6.631A pdb=" N ILE C 665 " --> pdb=" O ILE C 676 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE C 527 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 99 through 103 removed outlier: 3.825A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= W, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= X, first strand: chain 'D' and resid 400 through 403 removed outlier: 6.761A pdb=" N LEU D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL D 320 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG D 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU D 322 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP D 307 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 450 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 327 through 329 Processing sheet with id= Z, first strand: chain 'D' and resid 673 through 677 removed outlier: 6.646A pdb=" N ILE D 665 " --> pdb=" O ILE D 676 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 527 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.70 Time building geometry restraints manager: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8507 1.37 - 1.51: 7081 1.51 - 1.66: 9514 1.66 - 1.80: 123 1.80 - 1.95: 19 Bond restraints: 25244 Sorted by residual: bond pdb=" N ASN D 394 " pdb=" CA ASN D 394 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.64e+00 bond pdb=" N LYS D 220 " pdb=" CA LYS D 220 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.32e+00 bond pdb=" N LYS B 220 " pdb=" CA LYS B 220 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.20e-02 6.94e+03 6.00e+00 bond pdb=" N ARG A 458 " pdb=" CA ARG A 458 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.77e+00 bond pdb=" N ARG D 458 " pdb=" CA ARG D 458 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.36e+00 ... (remaining 25239 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 514 105.86 - 112.90: 14186 112.90 - 119.94: 8223 119.94 - 126.98: 11060 126.98 - 134.02: 281 Bond angle restraints: 34264 Sorted by residual: angle pdb=" N GLU D 72 " pdb=" CA GLU D 72 " pdb=" CB GLU D 72 " ideal model delta sigma weight residual 110.12 115.79 -5.67 1.47e+00 4.63e-01 1.49e+01 angle pdb=" CA ASP K 3 " pdb=" CB ASP K 3 " pdb=" CG ASP K 3 " ideal model delta sigma weight residual 112.60 108.75 3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" CA ASP M 3 " pdb=" CB ASP M 3 " pdb=" CG ASP M 3 " ideal model delta sigma weight residual 112.60 108.84 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA ASP L 3 " pdb=" CB ASP L 3 " pdb=" CG ASP L 3 " ideal model delta sigma weight residual 112.60 108.95 3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA ASP J 5 " pdb=" CB ASP J 5 " pdb=" CG ASP J 5 " ideal model delta sigma weight residual 112.60 109.30 3.30 1.00e+00 1.00e+00 1.09e+01 ... (remaining 34259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 13840 17.63 - 35.27: 1091 35.27 - 52.90: 225 52.90 - 70.53: 55 70.53 - 88.16: 22 Dihedral angle restraints: 15233 sinusoidal: 6113 harmonic: 9120 Sorted by residual: dihedral pdb=" CA THR C 496 " pdb=" C THR C 496 " pdb=" N ASN C 497 " pdb=" CA ASN C 497 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA THR D 496 " pdb=" C THR D 496 " pdb=" N ASN D 497 " pdb=" CA ASN D 497 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR B 660 " pdb=" C TYR B 660 " pdb=" N GLU B 661 " pdb=" CA GLU B 661 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 15230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2487 0.033 - 0.065: 927 0.065 - 0.098: 340 0.098 - 0.130: 223 0.130 - 0.163: 20 Chirality restraints: 3997 Sorted by residual: chirality pdb=" CA ASP J 2 " pdb=" N ASP J 2 " pdb=" C ASP J 2 " pdb=" CB ASP J 2 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CB ILE B 271 " pdb=" CA ILE B 271 " pdb=" CG1 ILE B 271 " pdb=" CG2 ILE B 271 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 3994 not shown) Planarity restraints: 4398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 458 " -0.231 9.50e-02 1.11e+02 1.04e-01 7.01e+00 pdb=" NE ARG B 458 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 458 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 458 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 458 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 60 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO C 61 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 60 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 61 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.030 5.00e-02 4.00e+02 ... (remaining 4395 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 17 2.05 - 2.76: 3909 2.76 - 3.48: 34889 3.48 - 4.19: 59553 4.19 - 4.90: 106499 Nonbonded interactions: 204867 Sorted by model distance: nonbonded pdb=" CG ASP M 5 " pdb=" N ARG M 102 " model vdw 1.339 3.350 nonbonded pdb=" CG ASP J 5 " pdb=" N ARG J 102 " model vdw 1.339 3.350 nonbonded pdb=" CG ASP K 5 " pdb=" N ARG K 102 " model vdw 1.339 3.350 nonbonded pdb=" CG ASP L 5 " pdb=" N ARG L 102 " model vdw 1.340 3.350 nonbonded pdb=" CG ASP L 3 " pdb=" N ARG L 101 " model vdw 1.340 3.350 ... (remaining 204862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 877 or resid 1001 through 1002 or resid 1004)) selection = (chain 'B' and (resid 1 through 877 or resid 1001 through 1002 or resid 1004)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 724 or resid 1001 through 1005)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 16.950 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 66.620 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.180 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:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25244 Z= 0.213 Angle : 0.562 8.131 34264 Z= 0.303 Chirality : 0.045 0.163 3997 Planarity : 0.004 0.104 4398 Dihedral : 13.863 88.165 9419 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 0.27 % Allowed : 0.42 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3202 helix: 1.56 (0.15), residues: 1242 sheet: 0.04 (0.24), residues: 480 loop : -0.99 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 278 HIS 0.009 0.001 HIS B 586 PHE 0.009 0.001 PHE D 480 TYR 0.015 0.001 TYR A 252 ARG 0.011 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 224 time to evaluate : 2.589 Fit side-chains revert: symmetry clash REVERT: A 269 ARG cc_start: 0.5725 (ptt-90) cc_final: 0.5356 (pmt170) REVERT: C 160 GLN cc_start: 0.8274 (tt0) cc_final: 0.8070 (tm-30) REVERT: C 168 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 1006 ASP cc_start: 0.5787 (OUTLIER) cc_final: 0.5507 (m-30) REVERT: J 102 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5379 (ttt-90) REVERT: K 102 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6120 (ttt-90) REVERT: M 102 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6542 (ttm-80) outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 1.4127 time to fit residues: 374.0756 Evaluate side-chains 161 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 1006 ASP Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain M residue 102 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 25244 Z= 0.489 Angle : 0.630 8.176 34264 Z= 0.329 Chirality : 0.049 0.193 3997 Planarity : 0.005 0.056 4398 Dihedral : 8.524 76.581 3675 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.00 % Favored : 95.97 % Rotamer: Outliers : 1.91 % Allowed : 7.99 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3202 helix: 1.19 (0.15), residues: 1244 sheet: -0.10 (0.24), residues: 440 loop : -1.11 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 278 HIS 0.006 0.001 HIS C 327 PHE 0.016 0.002 PHE C 480 TYR 0.019 0.002 TYR A 14 ARG 0.007 0.001 ARG M 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 2.972 Fit side-chains REVERT: A 25 MET cc_start: 0.8260 (ptt) cc_final: 0.7904 (ptm) REVERT: A 35 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7711 (tmtt) REVERT: A 118 ASN cc_start: 0.7156 (t0) cc_final: 0.6813 (t0) REVERT: A 269 ARG cc_start: 0.5630 (ptt-90) cc_final: 0.5152 (pmt170) REVERT: A 586 HIS cc_start: 0.6718 (OUTLIER) cc_final: 0.6067 (m90) REVERT: B 586 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.5861 (m90) REVERT: C 131 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6559 (ptp-110) REVERT: C 160 GLN cc_start: 0.8262 (tt0) cc_final: 0.8040 (tm-30) REVERT: C 247 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: C 278 TRP cc_start: 0.6373 (OUTLIER) cc_final: 0.5383 (m100) REVERT: C 443 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: D 537 ASN cc_start: 0.7325 (m-40) cc_final: 0.7103 (m110) REVERT: K 102 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.2819 (mpt-90) REVERT: M 102 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.5364 (ttm170) outliers start: 50 outliers final: 12 residues processed: 192 average time/residue: 1.3186 time to fit residues: 295.1844 Evaluate side-chains 166 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain M residue 102 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 240 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 312 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25244 Z= 0.193 Angle : 0.491 7.362 34264 Z= 0.259 Chirality : 0.044 0.185 3997 Planarity : 0.004 0.057 4398 Dihedral : 8.044 85.953 3667 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 1.30 % Allowed : 11.28 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3202 helix: 1.38 (0.15), residues: 1248 sheet: -0.13 (0.24), residues: 442 loop : -1.04 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 278 HIS 0.006 0.001 HIS C 327 PHE 0.011 0.001 PHE B 638 TYR 0.016 0.001 TYR C 33 ARG 0.003 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 2.692 Fit side-chains REVERT: A 25 MET cc_start: 0.8278 (ptt) cc_final: 0.7959 (ptm) REVERT: A 35 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7681 (tmtt) REVERT: A 269 ARG cc_start: 0.5605 (ptt-90) cc_final: 0.5211 (pmt170) REVERT: A 586 HIS cc_start: 0.6602 (OUTLIER) cc_final: 0.5962 (m90) REVERT: B 76 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8285 (mm) REVERT: B 586 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.5747 (m90) REVERT: C 76 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7631 (OUTLIER) REVERT: C 131 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6453 (ptp-170) REVERT: C 160 GLN cc_start: 0.8269 (tt0) cc_final: 0.8051 (tm-30) REVERT: C 278 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.5160 (m100) REVERT: C 661 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: K 102 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.2980 (mpt-90) outliers start: 34 outliers final: 10 residues processed: 177 average time/residue: 1.1954 time to fit residues: 249.4550 Evaluate side-chains 158 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain K residue 102 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 8.9990 chunk 217 optimal weight: 0.0170 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 82 optimal weight: 0.3980 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 327 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25244 Z= 0.250 Angle : 0.503 8.063 34264 Z= 0.263 Chirality : 0.045 0.175 3997 Planarity : 0.004 0.054 4398 Dihedral : 7.781 86.663 3661 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 2.29 % Allowed : 12.39 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3202 helix: 1.43 (0.15), residues: 1248 sheet: -0.21 (0.22), residues: 530 loop : -1.00 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 278 HIS 0.004 0.001 HIS A 327 PHE 0.011 0.001 PHE A 638 TYR 0.018 0.001 TYR C 33 ARG 0.003 0.000 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 144 time to evaluate : 2.863 Fit side-chains REVERT: A 25 MET cc_start: 0.8295 (ptt) cc_final: 0.7961 (ptm) REVERT: A 35 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7624 (tmtt) REVERT: A 269 ARG cc_start: 0.5652 (ptt-90) cc_final: 0.5179 (pmt170) REVERT: A 586 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.5867 (m90) REVERT: B 76 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8417 (mm) REVERT: B 586 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.5616 (m90) REVERT: C 76 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7647 (mm) REVERT: C 131 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6538 (ptp-170) REVERT: C 160 GLN cc_start: 0.8280 (tt0) cc_final: 0.8059 (tm-30) REVERT: C 247 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: C 278 TRP cc_start: 0.6643 (OUTLIER) cc_final: 0.5428 (m100) REVERT: C 661 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: D 458 ARG cc_start: 0.7912 (ptm160) cc_final: 0.7460 (ttm-80) REVERT: K 102 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.3502 (mpt-90) outliers start: 60 outliers final: 22 residues processed: 190 average time/residue: 1.1567 time to fit residues: 262.3479 Evaluate side-chains 173 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain K residue 102 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 126 optimal weight: 0.0000 chunk 262 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 25244 Z= 0.393 Angle : 0.558 8.303 34264 Z= 0.293 Chirality : 0.047 0.171 3997 Planarity : 0.004 0.054 4398 Dihedral : 7.896 87.182 3661 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 2.49 % Allowed : 13.54 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3202 helix: 1.31 (0.15), residues: 1254 sheet: -0.19 (0.24), residues: 460 loop : -1.05 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 278 HIS 0.007 0.001 HIS C 327 PHE 0.014 0.002 PHE C 480 TYR 0.017 0.002 TYR C 33 ARG 0.004 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 143 time to evaluate : 2.832 Fit side-chains REVERT: A 25 MET cc_start: 0.8278 (ptt) cc_final: 0.7956 (ptm) REVERT: A 35 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7603 (tmtt) REVERT: A 118 ASN cc_start: 0.7063 (t0) cc_final: 0.6715 (t0) REVERT: A 269 ARG cc_start: 0.5605 (ptt-90) cc_final: 0.5068 (pmt170) REVERT: A 586 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.5838 (m90) REVERT: B 1 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7566 (mpp) REVERT: B 32 LEU cc_start: 0.8812 (mp) cc_final: 0.8252 (mt) REVERT: B 76 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8397 (mm) REVERT: B 586 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.5586 (m90) REVERT: C 76 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7768 (mm) REVERT: C 131 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6623 (ptp-170) REVERT: C 247 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: C 278 TRP cc_start: 0.6667 (OUTLIER) cc_final: 0.5546 (m100) REVERT: C 443 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: C 661 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7560 (pt0) outliers start: 65 outliers final: 33 residues processed: 187 average time/residue: 1.1456 time to fit residues: 254.7826 Evaluate side-chains 184 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 307 optimal weight: 0.6980 chunk 255 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 327 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25244 Z= 0.220 Angle : 0.496 10.047 34264 Z= 0.259 Chirality : 0.045 0.158 3997 Planarity : 0.004 0.056 4398 Dihedral : 7.658 87.329 3657 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 2.45 % Allowed : 14.07 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3202 helix: 1.45 (0.15), residues: 1254 sheet: -0.19 (0.23), residues: 502 loop : -1.01 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 278 HIS 0.003 0.001 HIS A 650 PHE 0.012 0.001 PHE A 638 TYR 0.015 0.001 TYR A 14 ARG 0.002 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 144 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8306 (ptt) cc_final: 0.7990 (ptm) REVERT: A 35 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7579 (tmtt) REVERT: A 269 ARG cc_start: 0.5455 (ptt-90) cc_final: 0.5027 (pmt170) REVERT: A 586 HIS cc_start: 0.6502 (OUTLIER) cc_final: 0.5809 (m90) REVERT: B 586 HIS cc_start: 0.6425 (OUTLIER) cc_final: 0.5487 (m90) REVERT: C 76 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7670 (mm) REVERT: C 131 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6607 (ptp-170) REVERT: C 211 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9073 (tp) REVERT: C 247 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: C 278 TRP cc_start: 0.6684 (OUTLIER) cc_final: 0.5464 (m100) REVERT: C 661 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: C 686 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7860 (mmm) outliers start: 64 outliers final: 30 residues processed: 196 average time/residue: 1.1649 time to fit residues: 272.4956 Evaluate side-chains 182 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 175 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 0.0020 chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25244 Z= 0.315 Angle : 0.525 8.497 34264 Z= 0.275 Chirality : 0.046 0.159 3997 Planarity : 0.004 0.055 4398 Dihedral : 7.683 87.088 3657 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.75 % Allowed : 14.26 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3202 helix: 1.41 (0.15), residues: 1254 sheet: -0.18 (0.22), residues: 520 loop : -1.01 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 278 HIS 0.004 0.001 HIS A 327 PHE 0.012 0.002 PHE C 480 TYR 0.021 0.001 TYR D 33 ARG 0.003 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 142 time to evaluate : 2.700 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8306 (ptt) cc_final: 0.7993 (ptm) REVERT: A 35 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7583 (tmtt) REVERT: A 269 ARG cc_start: 0.5423 (ptt-90) cc_final: 0.4966 (pmt170) REVERT: A 586 HIS cc_start: 0.6446 (OUTLIER) cc_final: 0.5748 (m90) REVERT: B 76 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8342 (mm) REVERT: B 586 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.5543 (m90) REVERT: C 76 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7712 (mm) REVERT: C 131 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6633 (ptp-170) REVERT: C 211 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9067 (tp) REVERT: C 247 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: C 278 TRP cc_start: 0.6725 (OUTLIER) cc_final: 0.5499 (m100) REVERT: C 661 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: C 686 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7871 (mmm) outliers start: 72 outliers final: 41 residues processed: 201 average time/residue: 1.1002 time to fit residues: 264.3946 Evaluate side-chains 191 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN C 327 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25244 Z= 0.265 Angle : 0.512 8.515 34264 Z= 0.268 Chirality : 0.045 0.166 3997 Planarity : 0.004 0.055 4398 Dihedral : 7.621 86.595 3657 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.79 % Allowed : 14.49 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3202 helix: 1.44 (0.15), residues: 1254 sheet: -0.25 (0.22), residues: 530 loop : -0.97 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 278 HIS 0.003 0.001 HIS A 327 PHE 0.011 0.001 PHE A 638 TYR 0.017 0.001 TYR A 14 ARG 0.002 0.000 ARG B 561 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 142 time to evaluate : 2.725 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8306 (ptt) cc_final: 0.7992 (ptm) REVERT: A 35 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7568 (tmtt) REVERT: A 269 ARG cc_start: 0.5354 (ptt-90) cc_final: 0.4421 (pmt170) REVERT: A 586 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5604 (m90) REVERT: B 586 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5459 (m90) REVERT: C 76 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7725 (mm) REVERT: C 131 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6629 (ptp-170) REVERT: C 211 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9065 (tp) REVERT: C 278 TRP cc_start: 0.6704 (OUTLIER) cc_final: 0.5267 (m100) REVERT: C 661 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: C 686 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7852 (mmm) REVERT: D 353 HIS cc_start: 0.4139 (OUTLIER) cc_final: 0.3492 (t70) REVERT: D 458 ARG cc_start: 0.7921 (ptm160) cc_final: 0.7678 (ptm160) REVERT: D 537 ASN cc_start: 0.7134 (m-40) cc_final: 0.6892 (m110) outliers start: 73 outliers final: 43 residues processed: 198 average time/residue: 1.0780 time to fit residues: 256.4297 Evaluate side-chains 193 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 140 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 HIS Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 267 optimal weight: 0.0970 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 0.1980 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 270 optimal weight: 0.8980 chunk 284 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25244 Z= 0.144 Angle : 0.479 13.920 34264 Z= 0.247 Chirality : 0.044 0.159 3997 Planarity : 0.004 0.056 4398 Dihedral : 7.283 85.845 3657 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.95 % Allowed : 15.33 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3202 helix: 1.63 (0.15), residues: 1248 sheet: -0.06 (0.23), residues: 462 loop : -1.01 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 278 HIS 0.002 0.000 HIS C 650 PHE 0.013 0.001 PHE B 638 TYR 0.014 0.001 TYR D 242 ARG 0.003 0.000 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 151 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8308 (ptt) cc_final: 0.8020 (ptm) REVERT: A 35 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7608 (tmtt) REVERT: A 269 ARG cc_start: 0.5445 (ptt-90) cc_final: 0.4814 (pmt170) REVERT: A 586 HIS cc_start: 0.6284 (OUTLIER) cc_final: 0.5598 (m90) REVERT: B 732 MET cc_start: 0.6333 (mmp) cc_final: 0.5957 (mmp) REVERT: C 76 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7579 (mm) REVERT: C 131 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6549 (ptp-170) REVERT: C 211 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9073 (tp) REVERT: C 278 TRP cc_start: 0.6772 (OUTLIER) cc_final: 0.5371 (m100) REVERT: C 661 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: D 109 VAL cc_start: 0.8344 (t) cc_final: 0.8089 (t) REVERT: D 537 ASN cc_start: 0.6957 (m-40) cc_final: 0.6729 (m110) outliers start: 51 outliers final: 28 residues processed: 192 average time/residue: 1.1286 time to fit residues: 260.2210 Evaluate side-chains 177 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 143 optimal weight: 0.4980 chunk 209 optimal weight: 20.0000 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25244 Z= 0.249 Angle : 0.507 9.604 34264 Z= 0.264 Chirality : 0.045 0.242 3997 Planarity : 0.004 0.055 4398 Dihedral : 7.332 83.883 3657 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.84 % Allowed : 15.79 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3202 helix: 1.54 (0.15), residues: 1262 sheet: -0.13 (0.23), residues: 502 loop : -1.03 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 278 HIS 0.003 0.001 HIS A 327 PHE 0.011 0.001 PHE C 480 TYR 0.018 0.001 TYR A 14 ARG 0.002 0.000 ARG A 731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 140 time to evaluate : 2.707 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.8297 (ptt) cc_final: 0.7997 (ptm) REVERT: A 35 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7543 (tmtt) REVERT: A 269 ARG cc_start: 0.5398 (ptt-90) cc_final: 0.4423 (pmt170) REVERT: A 586 HIS cc_start: 0.6279 (OUTLIER) cc_final: 0.5558 (m90) REVERT: B 353 HIS cc_start: 0.2251 (OUTLIER) cc_final: 0.0318 (t70) REVERT: B 586 HIS cc_start: 0.6335 (OUTLIER) cc_final: 0.5354 (m90) REVERT: C 76 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7670 (mm) REVERT: C 131 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6630 (ptp-170) REVERT: C 211 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9135 (tp) REVERT: C 278 TRP cc_start: 0.6809 (OUTLIER) cc_final: 0.5403 (m100) REVERT: C 661 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: D 301 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7844 (ttt90) REVERT: D 537 ASN cc_start: 0.7081 (m-40) cc_final: 0.6847 (m110) outliers start: 48 outliers final: 30 residues processed: 180 average time/residue: 1.1422 time to fit residues: 244.9957 Evaluate side-chains 180 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 6.9990 chunk 268 optimal weight: 0.2980 chunk 77 optimal weight: 0.0060 chunk 232 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.0770 overall best weight: 0.6756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 327 HIS D 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092806 restraints weight = 38871.247| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.57 r_work: 0.3000 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25244 Z= 0.149 Angle : 0.477 9.468 34264 Z= 0.247 Chirality : 0.044 0.157 3997 Planarity : 0.004 0.055 4398 Dihedral : 7.087 81.733 3657 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.57 % Allowed : 15.98 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3202 helix: 1.62 (0.15), residues: 1262 sheet: 0.01 (0.24), residues: 462 loop : -1.05 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 278 HIS 0.002 0.000 HIS D 308 PHE 0.012 0.001 PHE B 638 TYR 0.011 0.001 TYR D 242 ARG 0.003 0.000 ARG D 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7450.81 seconds wall clock time: 133 minutes 38.71 seconds (8018.71 seconds total)