Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 07:45:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/04_2023/7wae_32383_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/04_2023/7wae_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_32383/04_2023/7wae_32383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/04_2023/7wae_32383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/04_2023/7wae_32383_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wae_32383/04_2023/7wae_32383_updated.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 12.57, per 1000 atoms: 0.51 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: 10.80 Conformation dependent library (CDL) restraints added in 3.5 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: 3.75 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: 10.02 Time building geometry restraints manager: 11.43 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: 13810 17.63 - 35.27: 1058 35.27 - 52.90: 210 52.90 - 70.53: 45 70.53 - 88.16: 22 Dihedral angle restraints: 15145 sinusoidal: 6025 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 15142 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: 3.870 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: 17.750 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 63.970 Find NCS groups from input model: 1.730 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.870 ------------------------------------------------------------------------------- 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 : 13.579 88.165 9331 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 % 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 *********************** 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 : 2.979 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 1.4736 time to fit residues: 390.4295 Evaluate side-chains 156 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 3.120 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4762 time to fit residues: 5.6749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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** ** B 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: 0.8523 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 25244 Z= 0.493 Angle : 0.632 7.946 34264 Z= 0.331 Chirality : 0.050 0.190 3997 Planarity : 0.005 0.058 4398 Dihedral : 7.090 79.041 3569 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer Outliers : 1.68 % 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: 1.18 (0.15), residues: 1246 sheet: -0.10 (0.24), residues: 440 loop : -1.12 (0.15), residues: 1516 *********************** 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 201 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 3.002 Fit side-chains outliers start: 44 outliers final: 10 residues processed: 188 average time/residue: 1.3969 time to fit residues: 307.6105 Evaluate side-chains 155 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 1 average time/residue: 0.2751 time to fit residues: 4.5949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** D 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25244 Z= 0.231 Angle : 0.497 7.122 34264 Z= 0.263 Chirality : 0.045 0.188 3997 Planarity : 0.004 0.057 4398 Dihedral : 6.854 87.599 3569 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer Outliers : 1.64 % 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: 0.06 (0.15), residues: 3202 helix: 1.37 (0.15), residues: 1248 sheet: -0.13 (0.24), residues: 442 loop : -1.05 (0.15), residues: 1512 *********************** 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 199 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 2.948 Fit side-chains outliers start: 43 outliers final: 19 residues processed: 186 average time/residue: 1.1751 time to fit residues: 259.8201 Evaluate side-chains 165 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 0.2558 time to fit residues: 5.4231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 0.5980 chunk 307 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 275 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 HIS ** 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: 0.8489 moved from start: 0.1437 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= 0.247 Angle : 0.503 7.986 34264 Z= 0.263 Chirality : 0.045 0.167 3997 Planarity : 0.004 0.055 4398 Dihedral : 6.796 89.164 3569 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer Outliers : 2.03 % 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: 1.44 (0.15), residues: 1246 sheet: -0.19 (0.22), residues: 530 loop : -0.99 (0.15), residues: 1426 *********************** 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 201 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 148 time to evaluate : 3.066 Fit side-chains outliers start: 53 outliers final: 22 residues processed: 191 average time/residue: 1.2046 time to fit residues: 275.1256 Evaluate side-chains 166 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 3.122 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.2903 time to fit residues: 5.0973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 262 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 25244 Z= 0.359 Angle : 0.547 8.039 34264 Z= 0.289 Chirality : 0.047 0.166 3997 Planarity : 0.004 0.055 4398 Dihedral : 6.942 89.293 3569 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer Outliers : 2.26 % 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: 0.04 (0.14), residues: 3202 helix: 1.35 (0.15), residues: 1242 sheet: -0.22 (0.24), residues: 462 loop : -1.03 (0.15), residues: 1498 *********************** 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 203 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 144 time to evaluate : 3.017 Fit side-chains outliers start: 59 outliers final: 31 residues processed: 188 average time/residue: 1.1804 time to fit residues: 266.3935 Evaluate side-chains 170 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.5723 time to fit residues: 7.7555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 307 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8478 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 25244 Z= 0.181 Angle : 0.478 7.548 34264 Z= 0.251 Chirality : 0.044 0.159 3997 Planarity : 0.004 0.056 4398 Dihedral : 6.722 89.480 3569 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer Outliers : 2.33 % 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: 0.18 (0.15), residues: 3202 helix: 1.52 (0.15), residues: 1248 sheet: -0.17 (0.23), residues: 502 loop : -1.02 (0.15), residues: 1452 *********************** 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: 61 poor density : 147 time to evaluate : 3.022 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 196 average time/residue: 1.2208 time to fit residues: 286.7135 Evaluate side-chains 176 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 2 average time/residue: 0.2739 time to fit residues: 5.1279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 224 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 25244 Z= 0.372 Angle : 0.555 8.363 34264 Z= 0.291 Chirality : 0.047 0.187 3997 Planarity : 0.004 0.054 4398 Dihedral : 6.923 89.242 3569 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 2.75 % 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: 0.06 (0.15), residues: 3202 helix: 1.36 (0.15), residues: 1254 sheet: -0.23 (0.22), residues: 522 loop : -1.04 (0.15), residues: 1426 *********************** 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 215 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 143 time to evaluate : 3.061 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 40 residues processed: 202 average time/residue: 1.1429 time to fit residues: 278.9956 Evaluate side-chains 181 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 2.782 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 3 average time/residue: 0.2688 time to fit residues: 5.3361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 183 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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: 0.8510 moved from start: 0.1939 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= 0.317 Angle : 0.535 11.721 34264 Z= 0.280 Chirality : 0.046 0.158 3997 Planarity : 0.004 0.055 4398 Dihedral : 6.915 88.715 3569 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 2.29 % 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: 0.05 (0.15), residues: 3202 helix: 1.37 (0.15), residues: 1254 sheet: -0.25 (0.22), residues: 522 loop : -1.06 (0.15), residues: 1426 *********************** 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 203 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 143 time to evaluate : 3.214 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 42 residues processed: 197 average time/residue: 1.1033 time to fit residues: 264.5490 Evaluate side-chains 178 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 3.118 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 40 residues processed: 2 average time/residue: 0.4296 time to fit residues: 5.5611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 267 optimal weight: 0.7980 chunk 285 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 284 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS D 537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 25244 Z= 0.155 Angle : 0.479 8.186 34264 Z= 0.250 Chirality : 0.044 0.171 3997 Planarity : 0.004 0.056 4398 Dihedral : 6.648 88.361 3569 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 2.03 % 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: 0.23 (0.15), residues: 3202 helix: 1.58 (0.15), residues: 1248 sheet: -0.16 (0.23), residues: 504 loop : -1.00 (0.15), residues: 1450 *********************** 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 203 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 150 time to evaluate : 2.913 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 38 residues processed: 198 average time/residue: 1.1143 time to fit residues: 269.0700 Evaluate side-chains 179 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 2.946 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 36 residues processed: 2 average time/residue: 0.2816 time to fit residues: 5.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 chunk 184 optimal weight: 0.0570 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 0.3980 chunk 252 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 overall best weight: 0.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 HIS ** 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: 0.8446 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 25244 Z= 0.132 Angle : 0.482 13.804 34264 Z= 0.247 Chirality : 0.043 0.159 3997 Planarity : 0.004 0.056 4398 Dihedral : 6.470 86.164 3569 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 1.72 % 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: 1.64 (0.15), residues: 1260 sheet: 0.00 (0.23), residues: 462 loop : -1.06 (0.15), residues: 1480 ********************** 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 194 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 3.113 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 37 residues processed: 190 average time/residue: 1.1170 time to fit residues: 256.8716 Evaluate side-chains 177 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 2.904 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 35 residues processed: 2 average time/residue: 0.2340 time to fit residues: 4.8149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.091379 restraints weight = 38906.467| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.55 r_work: 0.2961 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 25244 Z= 0.231 Angle : 0.505 9.593 34264 Z= 0.263 Chirality : 0.045 0.191 3997 Planarity : 0.004 0.054 4398 Dihedral : 6.567 85.149 3569 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 1.80 % 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: 1.61 (0.15), residues: 1260 sheet: -0.13 (0.22), residues: 532 loop : -0.99 (0.15), residues: 1410 =============================================================================== Job complete usr+sys time: 7159.09 seconds wall clock time: 129 minutes 1.94 seconds (7741.94 seconds total)