Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 05:52:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/04_2023/6b70_7062.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/04_2023/6b70_7062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/04_2023/6b70_7062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/04_2023/6b70_7062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/04_2023/6b70_7062.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/04_2023/6b70_7062.pdb" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 14201 2.51 5 N 3718 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 212": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22192 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7748 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 897} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7677 Classifications: {'peptide': 940} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 890} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1624 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Chain: "D" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1623 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1624 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Chain: "F" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1623 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "a" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "c" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 111 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASN C 207 " occ=0.84 ... (6 atoms not shown) pdb=" ND2 ASN C 207 " occ=0.84 residue: pdb=" N THR D 23 " occ=0.95 ... (5 atoms not shown) pdb=" CG2 THR D 23 " occ=0.95 residue: pdb=" N LYS D 46 " occ=0.91 ... (7 atoms not shown) pdb=" NZ LYS D 46 " occ=0.91 residue: pdb=" N GLU D 106 " occ=0.95 ... (7 atoms not shown) pdb=" OE2 GLU D 106 " occ=0.95 residue: pdb=" N ASN E 207 " occ=0.84 ... (6 atoms not shown) pdb=" ND2 ASN E 207 " occ=0.84 residue: pdb=" N THR F 23 " occ=0.95 ... (5 atoms not shown) pdb=" CG2 THR F 23 " occ=0.95 residue: pdb=" N LYS F 46 " occ=0.91 ... (7 atoms not shown) pdb=" NZ LYS F 46 " occ=0.91 residue: pdb=" N GLU F 106 " occ=0.95 ... (7 atoms not shown) pdb=" OE2 GLU F 106 " occ=0.95 Time building chain proxies: 11.28, per 1000 atoms: 0.51 Number of scatterers: 22192 At special positions: 0 Unit cell: (162.023, 163.096, 150.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 4203 8.00 N 3718 7.00 C 14201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 11 " distance=2.05 Simple disulfide: pdb=" SG CYS c 6 " - pdb=" SG CYS c 11 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.60 Conformation dependent library (CDL) restraints added in 3.4 seconds 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 35 sheets defined 33.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.613A pdb=" N PHE A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 167 removed outlier: 4.058A pdb=" N GLN A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 192 removed outlier: 3.613A pdb=" N LYS A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.015A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.811A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.730A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.640A pdb=" N GLU A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.668A pdb=" N LEU A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 4.024A pdb=" N VAL A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 516 removed outlier: 3.942A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 4.475A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.744A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 708 through 720 Proline residue: A 717 - end of helix Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 815 removed outlier: 3.696A pdb=" N MET A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 823 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.586A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 3.524A pdb=" N PHE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 913 removed outlier: 3.833A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.527A pdb=" N THR A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 929 " --> pdb=" O VAL A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 944 removed outlier: 4.294A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 4.490A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 116 removed outlier: 3.883A pdb=" N PHE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 116 " --> pdb=" O HIS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.848A pdb=" N ALA B 161 " --> pdb=" O HIS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.816A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 3.732A pdb=" N ASP B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.794A pdb=" N LYS B 217 " --> pdb=" O PRO B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.726A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.804A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.842A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.610A pdb=" N TYR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.650A pdb=" N LEU B 384 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 385 " --> pdb=" O GLU B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 385' Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 407 through 424 removed outlier: 3.764A pdb=" N PHE B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 460 through 469 Processing helix chain 'B' and resid 470 through 471 No H-bonds generated for 'chain 'B' and resid 470 through 471' Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.906A pdb=" N VAL B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.567A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 4.405A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 585 " --> pdb=" O PHE B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 585' Processing helix chain 'B' and resid 586 through 614 removed outlier: 3.580A pdb=" N SER B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 Processing helix chain 'B' and resid 655 through 673 removed outlier: 3.739A pdb=" N ASN B 671 " --> pdb=" O MET B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.673A pdb=" N ALA B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 707 removed outlier: 4.011A pdb=" N VAL B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 708 through 721 Proline residue: B 717 - end of helix Processing helix chain 'B' and resid 734 through 754 removed outlier: 3.710A pdb=" N ASP B 747 " --> pdb=" O GLN B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.669A pdb=" N GLN B 762 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 763 " --> pdb=" O PRO B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 763' Processing helix chain 'B' and resid 801 through 823 removed outlier: 3.806A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) Proline residue: B 818 - end of helix Processing helix chain 'B' and resid 855 through 874 Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.822A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.523A pdb=" N LYS B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 removed outlier: 3.592A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1002 removed outlier: 4.369A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B1002 " --> pdb=" O PHE B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.875A pdb=" N THR C 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.828A pdb=" N THR E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.595A pdb=" N THR E 139 " --> pdb=" O SER E 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 183 through 188 removed outlier: 3.561A pdb=" N TYR F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 removed outlier: 3.548A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.934A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP A 553 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 731 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 621 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.770A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR A 779 " --> pdb=" O HIS A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 69 removed outlier: 4.107A pdb=" N ILE B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 258 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 148 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 150 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 152 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 137 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 303 through 304 removed outlier: 5.290A pdb=" N ILE B 304 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 491 through 492 removed outlier: 3.533A pdb=" N TYR B 500 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 549 through 553 removed outlier: 6.366A pdb=" N LEU B 559 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLY B 731 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS B 562 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 832 through 840 removed outlier: 4.109A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN B 844 " --> pdb=" O THR B 797 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.743A pdb=" N GLN C 6 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLY C 19 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.548A pdb=" N THR C 116 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE C 37 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.548A pdb=" N THR C 116 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.318A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.318A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AC1, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AC2, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.516A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR D 88 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 119 removed outlier: 5.544A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AC5, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'E' and resid 6 through 10 Processing sheet with id=AC7, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.597A pdb=" N TRP E 39 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER E 53 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE E 37 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.757A pdb=" N ARG E 101 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.658A pdb=" N GLY E 147 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS E 148 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 188 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 150 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.658A pdb=" N GLY E 147 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS E 148 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 188 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 150 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 161 through 162 removed outlier: 4.144A pdb=" N TYR E 202 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AD4, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.224A pdb=" N LEU F 12 " --> pdb=" O GLU F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 54 through 55 removed outlier: 6.397A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR F 98 " --> pdb=" O GLN F 91 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.551A pdb=" N ASN F 138 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER F 178 " --> pdb=" O CYS F 135 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 147 through 151 979 hydrogen bonds defined for protein. 2724 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.81 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7117 1.34 - 1.48: 6041 1.48 - 1.61: 9456 1.61 - 1.75: 0 1.75 - 1.88: 117 Bond restraints: 22731 Sorted by residual: bond pdb=" C PHE A 317 " pdb=" N PRO A 318 " ideal model delta sigma weight residual 1.334 1.293 0.041 1.11e-02 8.12e+03 1.35e+01 bond pdb=" CB VAL A 186 " pdb=" CG2 VAL A 186 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.00e+00 bond pdb=" CB ASN A 591 " pdb=" CG ASN A 591 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.27e+00 bond pdb=" CB TRP A 908 " pdb=" CG TRP A 908 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.12e+00 bond pdb=" CB VAL E 51 " pdb=" CG2 VAL E 51 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.96e+00 ... (remaining 22726 not shown) Histogram of bond angle deviations from ideal: 95.61 - 104.34: 428 104.34 - 113.08: 12377 113.08 - 121.82: 13174 121.82 - 130.56: 4709 130.56 - 139.30: 118 Bond angle restraints: 30806 Sorted by residual: angle pdb=" N SER C 36 " pdb=" CA SER C 36 " pdb=" C SER C 36 " ideal model delta sigma weight residual 109.79 118.44 -8.65 1.56e+00 4.11e-01 3.08e+01 angle pdb=" C PHE E 154 " pdb=" N PRO E 155 " pdb=" CA PRO E 155 " ideal model delta sigma weight residual 127.00 139.30 -12.30 2.40e+00 1.74e-01 2.63e+01 angle pdb=" C CYS c 6 " pdb=" N CYS c 7 " pdb=" CA CYS c 7 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C ASP A 586 " pdb=" N PRO A 587 " pdb=" CA PRO A 587 " ideal model delta sigma weight residual 119.84 113.61 6.23 1.25e+00 6.40e-01 2.48e+01 angle pdb=" C PHE E 154 " pdb=" N PRO E 155 " pdb=" CD PRO E 155 " ideal model delta sigma weight residual 120.60 110.32 10.28 2.20e+00 2.07e-01 2.18e+01 ... (remaining 30801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 12874 17.57 - 35.15: 698 35.15 - 52.72: 128 52.72 - 70.29: 9 70.29 - 87.87: 10 Dihedral angle restraints: 13719 sinusoidal: 5545 harmonic: 8174 Sorted by residual: dihedral pdb=" CA PRO B 772 " pdb=" C PRO B 772 " pdb=" N ASP B 773 " pdb=" CA ASP B 773 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER B 171 " pdb=" C SER B 171 " pdb=" N PRO B 172 " pdb=" CA PRO B 172 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PRO C 131 " pdb=" C PRO C 131 " pdb=" N LEU C 132 " pdb=" CA LEU C 132 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 13716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2179 0.059 - 0.118: 937 0.118 - 0.177: 218 0.177 - 0.236: 35 0.236 - 0.294: 7 Chirality restraints: 3376 Sorted by residual: chirality pdb=" CB ILE B 319 " pdb=" CA ILE B 319 " pdb=" CG1 ILE B 319 " pdb=" CG2 ILE B 319 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB VAL A 153 " pdb=" CA VAL A 153 " pdb=" CG1 VAL A 153 " pdb=" CG2 VAL A 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA GLU A 503 " pdb=" N GLU A 503 " pdb=" C GLU A 503 " pdb=" CB GLU A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3373 not shown) Planarity restraints: 3965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 57 " 0.060 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO B 58 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 156 " 0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO C 157 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU a 16 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LEU a 16 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU a 16 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU a 17 " 0.019 2.00e-02 2.50e+03 ... (remaining 3962 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2521 2.73 - 3.27: 21158 3.27 - 3.82: 37805 3.82 - 4.36: 43136 4.36 - 4.90: 74345 Nonbonded interactions: 178965 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG1 THR A 268 " model vdw 2.192 2.440 nonbonded pdb=" O GLY C 141 " pdb=" OG SER C 194 " model vdw 2.218 2.440 nonbonded pdb=" OE1 GLU A 145 " pdb=" OH TYR A 443 " model vdw 2.252 2.440 nonbonded pdb=" OG SER A 87 " pdb=" O PHE A 151 " model vdw 2.257 2.440 nonbonded pdb=" O MET A 744 " pdb=" OG1 THR A 748 " model vdw 2.263 2.440 ... (remaining 178960 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 46 through 656 or (resid 657 and (name N or name CA or nam \ e C or name O or name CB )) or resid 658 through 704 or (resid 705 and (name N o \ r name CA or name C or name O or name CB )) or resid 706 through 763 or (resid 7 \ 64 through 765 and (name N or name CA or name C or name O or name CB )) or resid \ 766 through 962 or resid 989 through 1011)) selection = (chain 'B' and (resid 46 through 541 or (resid 542 through 544 and (name N or na \ me CA or name C or name O or name CB )) or resid 545 through 1011)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.010 Extract box with map and model: 8.550 Check model and map are aligned: 0.300 Set scattering table: 0.160 Process input model: 56.710 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.011 0.093 22731 Z= 0.729 Angle : 1.263 12.302 30806 Z= 0.679 Chirality : 0.067 0.294 3376 Planarity : 0.010 0.092 3965 Dihedral : 11.298 87.865 8423 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -3.94 (0.13), residues: 2763 helix: -2.86 (0.13), residues: 810 sheet: -2.09 (0.17), residues: 701 loop : -2.63 (0.15), residues: 1252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.4045 time to fit residues: 222.6462 Evaluate side-chains 143 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 245 HIS A 407 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 475 ASN B 724 HIS ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN D 125 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 87 ASN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN F 90 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 22731 Z= 0.230 Angle : 0.691 9.767 30806 Z= 0.360 Chirality : 0.045 0.306 3376 Planarity : 0.005 0.056 3965 Dihedral : 6.001 25.622 3013 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -2.25 (0.15), residues: 2763 helix: -0.88 (0.17), residues: 846 sheet: -1.27 (0.18), residues: 719 loop : -1.99 (0.17), residues: 1198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 232 average time/residue: 0.3516 time to fit residues: 128.5012 Evaluate side-chains 149 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 2.864 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2314 time to fit residues: 11.4419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 270 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN B 762 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 85 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 22731 Z= 0.483 Angle : 0.832 10.290 30806 Z= 0.427 Chirality : 0.048 0.323 3376 Planarity : 0.006 0.076 3965 Dihedral : 6.046 27.357 3013 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -1.84 (0.15), residues: 2763 helix: -0.28 (0.17), residues: 839 sheet: -1.26 (0.18), residues: 748 loop : -1.79 (0.18), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 124 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 34 residues processed: 180 average time/residue: 0.3418 time to fit residues: 99.5862 Evaluate side-chains 146 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 2.874 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2338 time to fit residues: 18.0173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 7.9990 chunk 188 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 167 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN D 167 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 22731 Z= 0.192 Angle : 0.616 9.106 30806 Z= 0.316 Chirality : 0.044 0.278 3376 Planarity : 0.004 0.050 3965 Dihedral : 5.422 24.372 3013 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -1.27 (0.16), residues: 2763 helix: 0.34 (0.18), residues: 842 sheet: -0.89 (0.19), residues: 736 loop : -1.61 (0.18), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 161 average time/residue: 0.3371 time to fit residues: 89.2149 Evaluate side-chains 124 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2369 time to fit residues: 5.7404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 22731 Z= 0.292 Angle : 0.652 7.966 30806 Z= 0.334 Chirality : 0.044 0.238 3376 Planarity : 0.004 0.048 3965 Dihedral : 5.367 24.620 3013 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -1.11 (0.16), residues: 2763 helix: 0.46 (0.18), residues: 847 sheet: -0.84 (0.19), residues: 746 loop : -1.48 (0.19), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 150 average time/residue: 0.3306 time to fit residues: 81.1344 Evaluate side-chains 134 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2060 time to fit residues: 8.4678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 266 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 22731 Z= 0.159 Angle : 0.603 15.182 30806 Z= 0.302 Chirality : 0.043 0.249 3376 Planarity : 0.004 0.046 3965 Dihedral : 5.045 23.779 3013 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -0.78 (0.16), residues: 2763 helix: 0.83 (0.18), residues: 841 sheet: -0.65 (0.19), residues: 736 loop : -1.36 (0.18), residues: 1186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 161 average time/residue: 0.3415 time to fit residues: 89.2445 Evaluate side-chains 134 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 2.795 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2036 time to fit residues: 6.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 265 optimal weight: 10.0000 chunk 165 optimal weight: 0.0030 chunk 161 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 overall best weight: 3.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN C 85 GLN D 156 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 22731 Z= 0.360 Angle : 0.704 13.009 30806 Z= 0.355 Chirality : 0.045 0.239 3376 Planarity : 0.005 0.048 3965 Dihedral : 5.266 25.001 3013 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -0.92 (0.16), residues: 2763 helix: 0.55 (0.18), residues: 847 sheet: -0.72 (0.19), residues: 755 loop : -1.33 (0.19), residues: 1161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 150 average time/residue: 0.3385 time to fit residues: 83.1385 Evaluate side-chains 132 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 2.649 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2108 time to fit residues: 8.9646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 ASN C 85 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 22731 Z= 0.193 Angle : 0.628 12.867 30806 Z= 0.312 Chirality : 0.043 0.236 3376 Planarity : 0.004 0.046 3965 Dihedral : 5.028 23.319 3013 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -0.69 (0.16), residues: 2763 helix: 0.81 (0.18), residues: 845 sheet: -0.55 (0.19), residues: 732 loop : -1.28 (0.18), residues: 1186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 137 average time/residue: 0.3533 time to fit residues: 79.0254 Evaluate side-chains 122 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2288 time to fit residues: 4.9230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 246 optimal weight: 30.0000 chunk 148 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 22731 Z= 0.368 Angle : 0.732 16.012 30806 Z= 0.366 Chirality : 0.045 0.231 3376 Planarity : 0.005 0.048 3965 Dihedral : 5.279 24.856 3013 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -0.92 (0.16), residues: 2763 helix: 0.53 (0.18), residues: 846 sheet: -0.68 (0.19), residues: 754 loop : -1.34 (0.19), residues: 1163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.3574 time to fit residues: 74.6149 Evaluate side-chains 122 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2200 time to fit residues: 6.6102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 5.9990 chunk 159 optimal weight: 0.0970 chunk 123 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 218 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN D 91 GLN D 167 GLN E 42 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22731 Z= 0.200 Angle : 0.664 16.318 30806 Z= 0.326 Chirality : 0.044 0.230 3376 Planarity : 0.004 0.045 3965 Dihedral : 5.044 22.981 3013 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -0.69 (0.16), residues: 2763 helix: 0.79 (0.18), residues: 845 sheet: -0.52 (0.19), residues: 732 loop : -1.28 (0.18), residues: 1186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 135 average time/residue: 0.3812 time to fit residues: 83.4462 Evaluate side-chains 119 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 2.889 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2239 time to fit residues: 4.3395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 32 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 191 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.063177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.048884 restraints weight = 113837.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050541 restraints weight = 52334.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051633 restraints weight = 30679.699| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 22731 Z= 0.160 Angle : 0.642 16.602 30806 Z= 0.312 Chirality : 0.043 0.213 3376 Planarity : 0.004 0.044 3965 Dihedral : 4.786 22.240 3013 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % 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: -0.47 (0.16), residues: 2763 helix: 1.01 (0.18), residues: 844 sheet: -0.48 (0.19), residues: 759 loop : -1.13 (0.19), residues: 1160 =============================================================================== Job complete usr+sys time: 3578.83 seconds wall clock time: 67 minutes 19.58 seconds (4039.58 seconds total)