Starting phenix.real_space_refine (version: dev) on Tue Feb 21 09:07:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2023/7k1s_22629.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2023/7k1s_22629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2023/7k1s_22629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2023/7k1s_22629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2023/7k1s_22629.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2023/7k1s_22629.pdb" } resolution = 3.9 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C GLU 663": "OE1" <-> "OE2" Residue "C GLU 694": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 716": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14409 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.46, per 1000 atoms: 0.59 Number of scatterers: 14409 At special positions: 0 Unit cell: (90.1, 96.46, 178.08, 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 66 16.00 O 2778 8.00 N 2478 7.00 C 9087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 540 " distance=2.02 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 540 " distance=2.02 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 540 " distance=2.02 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 645 " 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 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN E 3 " - " MAN E 6 " " MAN E 4 " - " MAN E 5 " " MAN F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN E 3 " - " MAN E 4 " " MAN F 3 " - " MAN F 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 686 " " NAG B1001 " - " ASN B 686 " " NAG C1001 " - " ASN C 686 " " NAG D 1 " - " ASN A 257 " " NAG E 1 " - " ASN B 257 " " NAG F 1 " - " ASN C 257 " Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 33 sheets defined 22.3% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.681A pdb=" N ILE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 554 removed outlier: 4.159A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'B' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 368' Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.682A pdb=" N ILE B 412 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 554 removed outlier: 3.872A pdb=" N GLN B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (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 702 through 707 Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'C' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 408 through 412 removed outlier: 3.681A pdb=" N ILE C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 554 removed outlier: 4.158A pdb=" N ALA C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 729 Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 574 removed outlier: 4.371A pdb=" N THR A 129 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 130 " --> pdb=" O GLY C 677 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 679 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG A 132 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 403 removed outlier: 6.092A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 403 removed outlier: 6.092A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR A 178 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 176 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 193 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 174 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG A 195 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 172 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 170 " --> pdb=" O PRO A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR A 178 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 176 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 193 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 174 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG A 195 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 172 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 170 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS A 166 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN A 360 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA9, first strand: chain 'A' and resid 591 through 595 removed outlier: 3.863A pdb=" N GLN A 628 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 636 " --> pdb=" O GLN A 628 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU A 663 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 677 through 679 removed outlier: 3.828A pdb=" N GLY A 677 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR B 129 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP B 374 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 157 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 376 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 155 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 378 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA B 153 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP B 374 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 157 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 376 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 155 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 378 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA B 153 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR B 178 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 191 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 176 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 193 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 174 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 195 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 172 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR B 170 " --> pdb=" O PRO B 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR B 178 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 191 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 176 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 193 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 174 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 195 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 172 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR B 170 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS B 166 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN B 360 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 212 through 214 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AC1, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AC2, first strand: chain 'B' and resid 591 through 595 removed outlier: 3.862A pdb=" N GLN B 628 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 636 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AC4, first strand: chain 'B' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU B 663 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 677 through 679 removed outlier: 3.750A pdb=" N GLY B 677 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR C 129 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP C 374 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS C 157 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 376 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 155 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 378 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA C 153 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP C 374 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS C 157 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 376 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 155 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 378 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA C 153 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS C 166 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN C 360 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 212 through 214 Processing sheet with id=AD2, first strand: chain 'C' and resid 216 through 221 Processing sheet with id=AD3, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AD4, first strand: chain 'C' and resid 591 through 595 removed outlier: 3.862A pdb=" N GLN C 628 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 636 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AD6, first strand: chain 'C' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU C 663 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1719 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: 5.20 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4680 1.34 - 1.46: 3625 1.46 - 1.58: 6332 1.58 - 1.70: 0 1.70 - 1.83: 102 Bond restraints: 14739 Sorted by residual: bond pdb=" N ILE B 679 " pdb=" CA ILE B 679 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 8.98e+00 bond pdb=" N ILE C 679 " pdb=" CA ILE C 679 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.84e+00 bond pdb=" N VAL C 512 " pdb=" CA VAL C 512 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.59e+00 bond pdb=" N ILE A 679 " pdb=" CA ILE A 679 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N MET B 678 " pdb=" CA MET B 678 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.33e+00 ... (remaining 14734 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.23: 363 106.23 - 113.17: 8173 113.17 - 120.12: 5055 120.12 - 127.06: 6266 127.06 - 134.01: 159 Bond angle restraints: 20016 Sorted by residual: angle pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 109.64 112.18 -2.54 5.38e-01 3.45e+00 2.24e+01 angle pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 109.64 112.08 -2.44 5.38e-01 3.45e+00 2.06e+01 angle pdb=" C2 NAG F 2 " pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 109.64 112.01 -2.37 5.38e-01 3.45e+00 1.94e+01 angle pdb=" N VAL A 512 " pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 113.07 107.60 5.47 1.37e+00 5.33e-01 1.59e+01 angle pdb=" N PHE A 514 " pdb=" CA PHE A 514 " pdb=" C PHE A 514 " ideal model delta sigma weight residual 111.71 107.77 3.94 1.15e+00 7.56e-01 1.17e+01 ... (remaining 20011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 8300 22.08 - 44.16: 485 44.16 - 66.24: 50 66.24 - 88.32: 33 88.32 - 110.40: 3 Dihedral angle restraints: 8871 sinusoidal: 3696 harmonic: 5175 Sorted by residual: dihedral pdb=" CB CYS B 608 " pdb=" SG CYS B 608 " pdb=" SG CYS B 645 " pdb=" CB CYS B 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.35 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS A 608 " pdb=" SG CYS A 608 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.35 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS C 608 " pdb=" SG CYS C 608 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.34 78.34 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 8868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 2268 0.184 - 0.368: 15 0.368 - 0.552: 0 0.552 - 0.735: 0 0.735 - 0.919: 3 Chirality restraints: 2286 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 MAN F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.11e+03 chirality pdb=" C1 MAN D 4 " pdb=" O6 MAN D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.90e+03 chirality pdb=" C1 MAN E 4 " pdb=" O6 MAN E 3 " pdb=" C2 MAN E 4 " pdb=" O5 MAN E 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.76e+03 ... (remaining 2283 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.266 2.00e-02 2.50e+03 2.22e-01 6.17e+02 pdb=" C7 NAG F 2 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.373 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.262 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C7 NAG E 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.365 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.187 2.00e-02 2.50e+03 1.54e-01 2.97e+02 pdb=" C7 NAG D 2 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 37 2.30 - 2.95: 6792 2.95 - 3.60: 19460 3.60 - 4.25: 32642 4.25 - 4.90: 55457 Nonbonded interactions: 114388 Sorted by model distance: nonbonded pdb=" OE2 GLU A 513 " pdb=" OE2 GLU B 513 " model vdw 1.647 3.040 nonbonded pdb=" CD2 LEU A 698 " pdb=" CG1 VAL C 512 " model vdw 1.722 3.880 nonbonded pdb=" OE1 GLU A 513 " pdb=" OE1 GLU B 513 " model vdw 1.767 3.040 nonbonded pdb=" OE2 GLU A 513 " pdb=" CD GLU B 513 " model vdw 1.903 3.270 nonbonded pdb=" CD1 LEU A 517 " pdb=" OE2 GLU B 513 " model vdw 2.121 3.460 ... (remaining 114383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9087 2.51 5 N 2478 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.640 Check model and map are aligned: 0.220 Process input model: 39.370 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.006 0.064 14739 Z= 0.396 Angle : 0.887 7.983 20016 Z= 0.512 Chirality : 0.064 0.919 2286 Planarity : 0.009 0.222 2541 Dihedral : 14.276 110.404 5496 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.18), residues: 1740 helix: -0.57 (0.28), residues: 303 sheet: -2.12 (0.21), residues: 471 loop : -1.91 (0.17), residues: 966 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 306 time to evaluate : 1.825 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: 6 outliers final: 0 residues processed: 312 average time/residue: 0.3308 time to fit residues: 142.0551 Evaluate side-chains 159 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.0980 chunk 131 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 405 ASN A 411 GLN A 525 GLN A 543 GLN A 628 GLN A 674 HIS A 724 HIS B 223 ASN B 411 GLN B 525 GLN B 543 GLN B 583 ASN B 628 GLN B 649 HIS B 674 HIS B 724 HIS C 223 ASN C 411 GLN C 525 GLN C 543 GLN C 583 ASN C 628 GLN C 649 HIS C 724 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 14739 Z= 0.218 Angle : 0.631 8.165 20016 Z= 0.334 Chirality : 0.045 0.203 2286 Planarity : 0.004 0.038 2541 Dihedral : 7.653 106.058 2148 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1740 helix: 0.60 (0.30), residues: 288 sheet: -1.34 (0.22), residues: 468 loop : -1.20 (0.18), residues: 984 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 217 average time/residue: 0.2774 time to fit residues: 87.6645 Evaluate side-chains 172 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1767 time to fit residues: 8.7814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 724 HIS B 254 HIS B 458 GLN B 583 ASN B 674 HIS B 724 HIS C 254 HIS C 458 GLN C 583 ASN C 724 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 14739 Z= 0.234 Angle : 0.581 8.843 20016 Z= 0.308 Chirality : 0.045 0.195 2286 Planarity : 0.004 0.039 2541 Dihedral : 7.491 104.963 2148 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1740 helix: 1.02 (0.32), residues: 288 sheet: -1.08 (0.23), residues: 465 loop : -0.97 (0.18), residues: 987 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 190 average time/residue: 0.2736 time to fit residues: 76.2969 Evaluate side-chains 161 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1254 time to fit residues: 5.0233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 724 HIS ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 HIS B 721 ASN B 724 HIS ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 HIS C 721 ASN C 724 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 14739 Z= 0.426 Angle : 0.716 8.089 20016 Z= 0.383 Chirality : 0.050 0.243 2286 Planarity : 0.005 0.041 2541 Dihedral : 7.564 103.557 2148 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1740 helix: 1.12 (0.32), residues: 273 sheet: -0.77 (0.24), residues: 459 loop : -1.21 (0.18), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 40 residues processed: 187 average time/residue: 0.2429 time to fit residues: 69.7269 Evaluate side-chains 178 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1319 time to fit residues: 12.1298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14739 Z= 0.211 Angle : 0.554 9.054 20016 Z= 0.294 Chirality : 0.044 0.232 2286 Planarity : 0.004 0.039 2541 Dihedral : 7.382 105.654 2148 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1740 helix: 1.55 (0.32), residues: 267 sheet: -0.70 (0.23), residues: 462 loop : -1.07 (0.18), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 161 average time/residue: 0.2586 time to fit residues: 63.5359 Evaluate side-chains 132 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1126 time to fit residues: 3.9695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 14739 Z= 0.235 Angle : 0.562 8.736 20016 Z= 0.297 Chirality : 0.044 0.208 2286 Planarity : 0.004 0.038 2541 Dihedral : 7.242 104.862 2148 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1740 helix: 1.87 (0.32), residues: 270 sheet: -0.55 (0.23), residues: 456 loop : -1.01 (0.18), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 149 average time/residue: 0.2423 time to fit residues: 56.0432 Evaluate side-chains 140 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1325 time to fit residues: 5.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 167 optimal weight: 0.4980 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 14739 Z= 0.205 Angle : 0.547 9.454 20016 Z= 0.288 Chirality : 0.043 0.218 2286 Planarity : 0.004 0.037 2541 Dihedral : 7.178 105.223 2148 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1740 helix: 1.89 (0.32), residues: 270 sheet: -0.48 (0.23), residues: 462 loop : -0.93 (0.19), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 136 average time/residue: 0.2347 time to fit residues: 49.8200 Evaluate side-chains 126 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1408 time to fit residues: 3.4102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 14739 Z= 0.253 Angle : 0.563 9.024 20016 Z= 0.298 Chirality : 0.044 0.219 2286 Planarity : 0.004 0.037 2541 Dihedral : 7.148 104.819 2148 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1740 helix: 1.84 (0.32), residues: 273 sheet: -0.45 (0.23), residues: 462 loop : -0.99 (0.19), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.891 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 143 average time/residue: 0.2449 time to fit residues: 54.9796 Evaluate side-chains 130 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1402 time to fit residues: 4.3195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 14739 Z= 0.372 Angle : 0.651 8.831 20016 Z= 0.345 Chirality : 0.047 0.273 2286 Planarity : 0.004 0.038 2541 Dihedral : 7.248 103.449 2148 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1740 helix: 1.55 (0.32), residues: 273 sheet: -0.48 (0.23), residues: 501 loop : -1.27 (0.18), residues: 966 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.781 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 134 average time/residue: 0.2477 time to fit residues: 52.0043 Evaluate side-chains 128 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1467 time to fit residues: 4.3340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 173 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14739 Z= 0.225 Angle : 0.568 9.103 20016 Z= 0.298 Chirality : 0.044 0.210 2286 Planarity : 0.004 0.040 2541 Dihedral : 7.197 105.011 2148 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1740 helix: 1.80 (0.32), residues: 273 sheet: -0.48 (0.23), residues: 495 loop : -1.12 (0.19), residues: 972 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.687 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 135 average time/residue: 0.2459 time to fit residues: 52.3824 Evaluate side-chains 125 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1203 time to fit residues: 3.6271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.155371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121889 restraints weight = 18392.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125720 restraints weight = 11310.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.128379 restraints weight = 7881.416| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 0.054 14739 Z= 0.204 Angle : 0.553 9.064 20016 Z= 0.289 Chirality : 0.043 0.183 2286 Planarity : 0.004 0.039 2541 Dihedral : 7.096 105.103 2148 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1740 helix: 1.97 (0.32), residues: 276 sheet: -0.34 (0.23), residues: 501 loop : -1.07 (0.19), residues: 963 =============================================================================== Job complete usr+sys time: 2495.48 seconds wall clock time: 46 minutes 29.66 seconds (2789.66 seconds total)