Starting phenix.real_space_refine on Thu Nov 16 22:06:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2023/8p3t_17394_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2023/8p3t_17394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2023/8p3t_17394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2023/8p3t_17394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2023/8p3t_17394_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2023/8p3t_17394_neut.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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 96 5.16 5 C 11054 2.51 5 N 2737 2.21 5 O 2974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "D PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H GLU 202": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16861 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2843 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 373} Chain breaks: 4 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 137 Chain: "B" Number of atoms: 2909 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 2878 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Conformer: "B" Number of residues, atoms: 384, 2878 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 bond proxies already assigned to first conformer: 2906 Chain: "C" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2840 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "D" Number of atoms: 2847 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 379, 2816 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 367} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 Conformer: "B" Number of residues, atoms: 379, 2816 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 367} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 bond proxies already assigned to first conformer: 2842 Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE B 570 " occ=0.54 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.46 residue: pdb=" N AGLN B 582 " occ=0.16 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.84 residue: pdb=" N APHE B 619 " occ=0.64 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.36 residue: pdb=" N APHE D 570 " occ=0.52 ... (20 atoms not shown) pdb=" CZ BPHE D 570 " occ=0.48 residue: pdb=" N AGLN D 582 " occ=0.26 ... (16 atoms not shown) pdb=" NE2BGLN D 582 " occ=0.74 residue: pdb=" N APHE D 619 " occ=0.53 ... (20 atoms not shown) pdb=" CZ BPHE D 619 " occ=0.47 Time building chain proxies: 12.38, per 1000 atoms: 0.73 Number of scatterers: 16861 At special positions: 0 Unit cell: (121.9, 112.625, 136.475, 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 96 16.00 O 2974 8.00 N 2737 7.00 C 11054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.02 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 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: 7.57 Conformation dependent library (CDL) restraints added in 4.5 seconds 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4094 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 26 sheets defined 61.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.559A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.086A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 removed outlier: 3.542A pdb=" N ARG A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.762A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.606A pdb=" N GLN B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 433 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.703A pdb=" N PHE B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 625 removed outlier: 3.565A pdb=" N VAL B 597 " --> pdb=" O SER B 593 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 623 " --> pdb=" O APHE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.524A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 702 through 711 Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.652A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.549A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.280A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 619 Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.519A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.823A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.567A pdb=" N GLN D 410 " --> pdb=" O ASN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.160A pdb=" N ASP D 415 " --> pdb=" O GLU D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 518 through 542 removed outlier: 3.631A pdb=" N PHE D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 removed outlier: 3.562A pdb=" N VAL D 597 " --> pdb=" O SER D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 638 Processing helix chain 'D' and resid 649 through 657 Processing helix chain 'D' and resid 660 through 673 removed outlier: 3.518A pdb=" N SER D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 702 through 711 Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.904A pdb=" N PHE D 792 " --> pdb=" O VAL D 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.120A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.723A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.510A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.970A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.862A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.559A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 removed outlier: 3.529A pdb=" N ALA G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 removed outlier: 3.671A pdb=" N LEU G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.680A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.839A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.665A pdb=" N LEU G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 4.158A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.655A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.587A pdb=" N ILE H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.626A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 3.671A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 494 removed outlier: 4.063A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.573A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.719A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.896A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.454A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.580A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.767A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.876A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.559A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.375A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC2, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC3, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.849A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.591A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'H' and resid 77 through 79 1114 hydrogen bonds defined for protein. 3251 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: 5.49 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2614 1.32 - 1.44: 4986 1.44 - 1.57: 9496 1.57 - 1.70: 0 1.70 - 1.83: 156 Bond restraints: 17252 Sorted by residual: bond pdb=" C SER A 631 " pdb=" O SER A 631 " ideal model delta sigma weight residual 1.235 1.311 -0.076 1.03e-02 9.43e+03 5.42e+01 bond pdb=" CA SER A 631 " pdb=" CB SER A 631 " ideal model delta sigma weight residual 1.532 1.475 0.058 1.28e-02 6.10e+03 2.03e+01 bond pdb=" N VAL C 484 " pdb=" CA VAL C 484 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.86e+01 bond pdb=" C MET B 499 " pdb=" O MET B 499 " ideal model delta sigma weight residual 1.235 1.283 -0.048 1.12e-02 7.97e+03 1.82e+01 bond pdb=" C TYR D 391 " pdb=" O TYR D 391 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.34e-02 5.57e+03 1.76e+01 ... (remaining 17247 not shown) Histogram of bond angle deviations from ideal: 86.83 - 96.37: 4 96.37 - 105.91: 312 105.91 - 115.46: 10219 115.46 - 125.00: 12445 125.00 - 134.54: 439 Bond angle restraints: 23419 Sorted by residual: angle pdb=" N LEU A 635 " pdb=" CA LEU A 635 " pdb=" C LEU A 635 " ideal model delta sigma weight residual 112.54 97.84 14.70 1.22e+00 6.72e-01 1.45e+02 angle pdb=" C LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta sigma weight residual 110.42 86.83 23.59 1.99e+00 2.53e-01 1.41e+02 angle pdb=" C THR A 639 " pdb=" CA THR A 639 " pdb=" CB THR A 639 " ideal model delta sigma weight residual 110.36 95.36 15.00 1.78e+00 3.16e-01 7.10e+01 angle pdb=" C GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta sigma weight residual 110.10 94.16 15.94 1.90e+00 2.77e-01 7.04e+01 angle pdb=" N ILE A 641 " pdb=" CA ILE A 641 " pdb=" C ILE A 641 " ideal model delta sigma weight residual 109.34 94.11 15.23 2.08e+00 2.31e-01 5.36e+01 ... (remaining 23414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8741 17.96 - 35.93: 877 35.93 - 53.89: 217 53.89 - 71.86: 45 71.86 - 89.82: 9 Dihedral angle restraints: 9889 sinusoidal: 3475 harmonic: 6414 Sorted by residual: dihedral pdb=" C LYS A 637 " pdb=" N LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta harmonic sigma weight residual -122.60 -94.65 -27.95 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" CD ARG A 624 " pdb=" NE ARG A 624 " pdb=" CZ ARG A 624 " pdb=" NH1 ARG A 624 " ideal model delta sinusoidal sigma weight residual 0.00 -65.68 65.68 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" C GLU C 630 " pdb=" N GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta harmonic sigma weight residual -122.60 -105.89 -16.71 0 2.50e+00 1.60e-01 4.47e+01 ... (remaining 9886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1722 0.099 - 0.199: 907 0.199 - 0.298: 58 0.298 - 0.398: 14 0.398 - 0.497: 3 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CA ILE B 500 " pdb=" N ILE B 500 " pdb=" C ILE B 500 " pdb=" CB ILE B 500 " both_signs ideal model delta sigma weight residual False 2.43 2.93 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA LYS A 637 " pdb=" N LYS A 637 " pdb=" C LYS A 637 " pdb=" CB LYS A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ILE D 500 " pdb=" N ILE D 500 " pdb=" C ILE D 500 " pdb=" CB ILE D 500 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2701 not shown) Planarity restraints: 2877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 624 " 0.947 9.50e-02 1.11e+02 4.25e-01 1.10e+02 pdb=" NE ARG A 624 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 624 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 624 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 624 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 630 " -0.033 2.00e-02 2.50e+03 7.05e-02 4.97e+01 pdb=" C GLU A 630 " 0.122 2.00e-02 2.50e+03 pdb=" O GLU A 630 " -0.047 2.00e-02 2.50e+03 pdb=" N SER A 631 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 632 " -0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ALA A 632 " 0.094 2.00e-02 2.50e+03 pdb=" O ALA A 632 " -0.036 2.00e-02 2.50e+03 pdb=" N GLU A 633 " -0.032 2.00e-02 2.50e+03 ... (remaining 2874 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2830 2.76 - 3.30: 17309 3.30 - 3.83: 27708 3.83 - 4.37: 33539 4.37 - 4.90: 56817 Nonbonded interactions: 138203 Sorted by model distance: nonbonded pdb=" O ALA A 636 " pdb=" N GLN A 638 " model vdw 2.226 2.520 nonbonded pdb=" OG SER A 631 " pdb=" N ALA A 632 " model vdw 2.237 2.520 nonbonded pdb=" OG1 THR G 30 " pdb=" OG SER G 178 " model vdw 2.238 2.440 nonbonded pdb=" N GLU G 95 " pdb=" OE1 GLU G 95 " model vdw 2.260 2.520 nonbonded pdb=" O LYS B 501 " pdb=" O LYS B 502 " model vdw 2.263 3.040 ... (remaining 138198 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 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 414 or (resid 415 through 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 429 or (resid 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 631 t \ hrough 664 or (resid 665 and (name N or name CA or name C or name O or name CB ) \ ) or resid 666 through 767 or resid 782 through 815)) selection = (chain 'B' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 415 or (res \ id 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 500 or (resid 501 through 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 509 through \ 545 or (resid 566 and (name N or name CA or name C or name O or name CB )) or r \ esid 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid \ 620 through 622 or resid 631 through 632 or (resid 633 through 634 and (name N o \ r name CA or name C or name O or name CB )) or resid 635 through 658 or (resid 6 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 660 through \ 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) or r \ esid 666 through 683 or (resid 684 and (name N or name CA or name C or name O or \ name CB )) or resid 685 through 687 or (resid 688 and (name N or name CA or nam \ e C or name O or name CB )) or resid 689 through 690 or (resid 691 through 693 a \ nd (name N or name CA or name C or name O or name CB )) or resid 694 through 705 \ or (resid 706 and (name N or name CA or name C or name O or name CB )) or resid \ 707 through 767 or resid 782 through 813 or (resid 814 through 815 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 415 or (resid 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 through 466 or (res \ id 467 through 469 and (name N or name CA or name C or name O or name CB )) or r \ esid 470 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 631 t \ hrough 633 or (resid 634 and (name N or name CA or name C or name O or name CB ) \ ) or resid 635 through 687 or (resid 688 and (name N or name CA or name C or nam \ e O or name CB )) or resid 689 through 691 or (resid 692 through 693 and (name N \ or name CA or name C or name O or name CB )) or resid 694 through 708 or (resid \ 709 and (name N or name CA or name C or name O or name CB )) or resid 710 throu \ gh 815)) selection = (chain 'D' and (resid 390 through 444 or (resid 445 and (name N or name CA or na \ me C or name O or name CB )) or resid 446 through 466 or (resid 467 through 469 \ and (name N or name CA or name C or name O or name CB )) or resid 470 through 54 \ 5 or (resid 566 and (name N or name CA or name C or name O or name CB )) or resi \ d 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid 620 \ through 658 or (resid 659 and (name N or name CA or name C or name O or name CB \ )) or resid 660 through 664 or (resid 665 and (name N or name CA or name C or n \ ame O or name CB )) or resid 666 through 687 or (resid 688 and (name N or name C \ A or name C or name O or name CB )) or resid 689 through 691 or (resid 692 throu \ gh 693 and (name N or name CA or name C or name O or name CB )) or resid 694 thr \ ough 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 708 or (resid 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 through 767 or resid 782 through 813 or (resid 814 \ through 815 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'E' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) selection = (chain 'F' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) selection = chain 'G' selection = (chain 'H' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) } 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=0.16 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: 1.050 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: 4.570 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 53.760 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 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:4.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.012 0.076 17252 Z= 0.752 Angle : 1.402 23.589 23419 Z= 1.028 Chirality : 0.102 0.497 2704 Planarity : 0.014 0.425 2877 Dihedral : 15.562 89.821 5771 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.54 % Favored : 97.09 % Rotamer: Outliers : 4.78 % Allowed : 17.33 % Favored : 77.88 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 23.08 % 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: -0.20 (0.16), residues: 2183 helix: 0.76 (0.13), residues: 1313 sheet: -2.80 (0.34), residues: 154 loop : -1.05 (0.21), residues: 716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 203 time to evaluate : 2.129 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: 79 outliers final: 44 residues processed: 274 average time/residue: 0.3460 time to fit residues: 135.5012 Evaluate side-chains 182 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.829 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1703 time to fit residues: 15.9952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN A 710 GLN B 710 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 160 ASN E 204 HIS F 160 ASN G 204 HIS H 9 GLN H 132 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17252 Z= 0.173 Angle : 0.550 8.861 23419 Z= 0.291 Chirality : 0.039 0.213 2704 Planarity : 0.004 0.052 2877 Dihedral : 3.609 30.242 2405 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.11 % Favored : 98.80 % Rotamer: Outliers : 2.09 % Allowed : 18.59 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.69 (0.18), residues: 2183 helix: 2.43 (0.14), residues: 1333 sheet: -1.67 (0.35), residues: 179 loop : -0.80 (0.22), residues: 671 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 2.017 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: 34 outliers final: 18 residues processed: 204 average time/residue: 0.3252 time to fit residues: 98.6548 Evaluate side-chains 156 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1656 time to fit residues: 8.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 135 optimal weight: 0.0270 chunk 54 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 GLN A C 615 ASN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17252 Z= 0.216 Angle : 0.532 12.376 23419 Z= 0.280 Chirality : 0.039 0.182 2704 Planarity : 0.003 0.052 2877 Dihedral : 3.449 25.461 2405 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.25 % Favored : 98.66 % Rotamer: Outliers : 2.03 % Allowed : 20.20 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.11 (0.18), residues: 2183 helix: 2.75 (0.14), residues: 1345 sheet: -1.83 (0.33), residues: 204 loop : -0.47 (0.24), residues: 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 2.002 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 outliers start: 32 outliers final: 10 residues processed: 176 average time/residue: 0.3270 time to fit residues: 84.5621 Evaluate side-chains 148 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1717 time to fit residues: 5.8335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17252 Z= 0.180 Angle : 0.510 11.615 23419 Z= 0.264 Chirality : 0.038 0.230 2704 Planarity : 0.003 0.041 2877 Dihedral : 3.324 17.946 2405 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.20 % Favored : 98.71 % Rotamer: Outliers : 1.67 % Allowed : 20.44 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.29 (0.19), residues: 2183 helix: 2.84 (0.14), residues: 1350 sheet: -1.45 (0.38), residues: 170 loop : -0.50 (0.23), residues: 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.872 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 outliers start: 26 outliers final: 7 residues processed: 177 average time/residue: 0.3013 time to fit residues: 80.8416 Evaluate side-chains 155 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1753 time to fit residues: 4.7708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 4.9990 chunk 120 optimal weight: 0.0010 chunk 3 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17252 Z= 0.300 Angle : 0.555 9.719 23419 Z= 0.294 Chirality : 0.040 0.239 2704 Planarity : 0.004 0.056 2877 Dihedral : 3.420 15.005 2405 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.67 % Allowed : 20.62 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 (0.19), residues: 2183 helix: 2.81 (0.14), residues: 1342 sheet: -1.47 (0.36), residues: 203 loop : -0.40 (0.24), residues: 638 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 2.002 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: 26 outliers final: 14 residues processed: 171 average time/residue: 0.2948 time to fit residues: 77.4546 Evaluate side-chains 151 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1595 time to fit residues: 6.9205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 30.0000 chunk 190 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN E 82 HIS E 160 ASN E 204 HIS F 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17252 Z= 0.155 Angle : 0.502 9.736 23419 Z= 0.262 Chirality : 0.038 0.225 2704 Planarity : 0.003 0.042 2877 Dihedral : 3.271 15.018 2405 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.39 % Favored : 98.57 % Rotamer: Outliers : 1.26 % Allowed : 20.92 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.49 (0.19), residues: 2183 helix: 3.00 (0.14), residues: 1342 sheet: -1.56 (0.38), residues: 171 loop : -0.34 (0.23), residues: 670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 168 average time/residue: 0.2950 time to fit residues: 76.8277 Evaluate side-chains 153 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1824 time to fit residues: 6.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 119 optimal weight: 50.0000 chunk 178 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 211 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17252 Z= 0.417 Angle : 0.620 12.503 23419 Z= 0.330 Chirality : 0.042 0.254 2704 Planarity : 0.004 0.042 2877 Dihedral : 3.570 14.819 2405 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 1.32 % Allowed : 21.82 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.16 (0.18), residues: 2183 helix: 2.68 (0.14), residues: 1341 sheet: -1.46 (0.40), residues: 152 loop : -0.41 (0.23), residues: 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 155 average time/residue: 0.2882 time to fit residues: 69.6207 Evaluate side-chains 138 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1617 time to fit residues: 6.4633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 0.0770 chunk 63 optimal weight: 0.0970 chunk 41 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 chunk 134 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 HIS F 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17252 Z= 0.150 Angle : 0.539 10.513 23419 Z= 0.276 Chirality : 0.039 0.233 2704 Planarity : 0.003 0.042 2877 Dihedral : 3.355 15.128 2405 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.39 % Favored : 98.57 % Rotamer: Outliers : 0.66 % Allowed : 22.47 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.50 (0.18), residues: 2183 helix: 2.97 (0.14), residues: 1342 sheet: -1.28 (0.45), residues: 126 loop : -0.38 (0.23), residues: 715 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 160 average time/residue: 0.3036 time to fit residues: 74.2666 Evaluate side-chains 146 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1705 time to fit residues: 3.6945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 60 optimal weight: 0.0570 chunk 177 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17252 Z= 0.271 Angle : 0.574 10.168 23419 Z= 0.300 Chirality : 0.039 0.255 2704 Planarity : 0.003 0.042 2877 Dihedral : 3.369 14.637 2405 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.29 % Rotamer: Outliers : 0.36 % Allowed : 22.30 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.43 (0.19), residues: 2183 helix: 2.85 (0.14), residues: 1346 sheet: -1.19 (0.43), residues: 142 loop : -0.30 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 145 average time/residue: 0.2754 time to fit residues: 63.6673 Evaluate side-chains 136 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1732 time to fit residues: 3.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 218 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17252 Z= 0.180 Angle : 0.573 10.489 23419 Z= 0.294 Chirality : 0.039 0.237 2704 Planarity : 0.003 0.042 2877 Dihedral : 3.397 15.673 2405 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.62 % Favored : 98.34 % Rotamer: Outliers : 0.42 % Allowed : 22.95 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.42 (0.19), residues: 2183 helix: 2.86 (0.14), residues: 1346 sheet: -1.37 (0.43), residues: 134 loop : -0.30 (0.23), residues: 703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4366 Ramachandran restraints generated. 2183 Oldfield, 0 Emsley, 2183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 144 average time/residue: 0.2641 time to fit residues: 60.7975 Evaluate side-chains 144 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1804 time to fit residues: 4.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 178 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN ** H 149 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 = 0.4175 r_free = 0.4175 target = 0.121684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075988 restraints weight = 143893.342| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 7.29 r_work: 0.2864 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17252 Z= 0.393 Angle : 0.636 10.718 23419 Z= 0.337 Chirality : 0.041 0.269 2704 Planarity : 0.004 0.041 2877 Dihedral : 3.561 16.437 2405 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.88 % Rotamer: Outliers : 0.36 % Allowed : 23.01 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 2.18 (0.19), residues: 2183 helix: 2.62 (0.14), residues: 1345 sheet: -1.40 (0.42), residues: 144 loop : -0.29 (0.24), residues: 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.77 seconds wall clock time: 62 minutes 32.99 seconds (3752.99 seconds total)