Starting phenix.real_space_refine on Thu Nov 16 22:50:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2023/8cxi_27058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2023/8cxi_27058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2023/8cxi_27058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2023/8cxi_27058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2023/8cxi_27058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2023/8cxi_27058.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 98 atoms to isotropic. 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 114 5.16 5 C 10612 2.51 5 N 2902 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "l PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 81": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1036 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 743 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.98, per 1000 atoms: 0.53 Number of scatterers: 16832 At special positions: 0 Unit cell: (106, 203.52, 121.9, 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 114 16.00 O 3204 8.00 N 2902 7.00 C 10612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.95 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.31 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=1.90 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=0.96 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.82 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.05 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=2.93 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 Atom "HETATM16746 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " NAG-ASN " NAG G 1 " - " ASN A 154 " Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 3.0 seconds 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 40 sheets defined 23.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 461 through 478 Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.535A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.563A pdb=" N LEU D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 97 through 100B removed outlier: 4.058A pdb=" N TYR H 100A" --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 27C through 32 removed outlier: 3.930A pdb=" N ASN L 31 " --> pdb=" O ALA L 27C" (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 32 " --> pdb=" O ASP L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 27C through 32' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.985A pdb=" N ILE B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.923A pdb=" N GLU B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.781A pdb=" N VAL B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 426 through 429 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.956A pdb=" N THR E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.910A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.553A pdb=" N LYS E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 83 through 87 removed outlier: 3.508A pdb=" N ASP h 86 " --> pdb=" O THR h 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 33 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.605A pdb=" N GLU l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.872A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 483 through 500 removed outlier: 3.566A pdb=" N LEU C 498 " --> pdb=" O VAL C 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 11 removed outlier: 3.604A pdb=" N LYS F 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 Processing helix chain 'F' and resid 40 through 52 Processing helix chain 'F' and resid 56 through 74 removed outlier: 3.702A pdb=" N LYS F 60 " --> pdb=" O SER F 56 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.684A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N MET A 125 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 58 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 127 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 54 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.684A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 26 removed outlier: 4.511A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.982A pdb=" N SER A 112 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA6, first strand: chain 'A' and resid 243 through 247 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.587A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.587A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.399A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.716A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 48 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 281 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 276 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 54 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.716A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 138 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 48 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU B 136 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.434A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 72 removed outlier: 6.411A pdb=" N LYS B 118 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 116 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 114 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 112 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 320 removed outlier: 7.088A pdb=" N THR B 315 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLN B 331 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE B 317 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 329 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.859A pdb=" N CYS B 339 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 365 " --> pdb=" O CYS B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC7, first strand: chain 'h' and resid 3 through 7 removed outlier: 3.635A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.555A pdb=" N TRP h 33 " --> pdb=" O ASP h 95 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET h 34 " --> pdb=" O ARG h 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 11 through 12 removed outlier: 4.509A pdb=" N VAL h 102 " --> pdb=" O ARG h 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 9 through 12 removed outlier: 7.123A pdb=" N VAL l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP l 35 " --> pdb=" O MET l 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 9 through 12 removed outlier: 7.123A pdb=" N VAL l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.606A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 127 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 54 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.606A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG C 138 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR C 48 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 20 through 26 Processing sheet with id=AD7, first strand: chain 'C' and resid 63 through 65 Processing sheet with id=AD8, first strand: chain 'C' and resid 63 through 65 Processing sheet with id=AD9, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AE1, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AE4, first strand: chain 'C' and resid 343 through 346 753 hydrogen bonds defined for protein. 1968 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: 5.97 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2730 1.27 - 1.41: 4286 1.41 - 1.54: 9975 1.54 - 1.68: 26 1.68 - 1.81: 179 Bond restraints: 17196 Sorted by residual: bond pdb=" CA SER C 72 " pdb=" C SER C 72 " ideal model delta sigma weight residual 1.520 1.415 0.105 1.20e-02 6.94e+03 7.65e+01 bond pdb=" CA MET A 125 " pdb=" C MET A 125 " ideal model delta sigma weight residual 1.522 1.425 0.098 1.19e-02 7.06e+03 6.78e+01 bond pdb=" C ARG C 73 " pdb=" O ARG C 73 " ideal model delta sigma weight residual 1.234 1.139 0.095 1.20e-02 6.94e+03 6.27e+01 bond pdb=" C MET A 125 " pdb=" O MET A 125 " ideal model delta sigma weight residual 1.235 1.146 0.089 1.23e-02 6.61e+03 5.26e+01 bond pdb=" CA LYS A 316 " pdb=" C LYS A 316 " ideal model delta sigma weight residual 1.522 1.426 0.095 1.37e-02 5.33e+03 4.83e+01 ... (remaining 17191 not shown) Histogram of bond angle deviations from ideal: 94.59 - 102.77: 116 102.77 - 110.95: 6778 110.95 - 119.13: 7479 119.13 - 127.32: 8702 127.32 - 135.50: 229 Bond angle restraints: 23304 Sorted by residual: angle pdb=" C CYS B 74 " pdb=" N PRO B 75 " pdb=" CA PRO B 75 " ideal model delta sigma weight residual 119.84 135.50 -15.66 1.25e+00 6.40e-01 1.57e+02 angle pdb=" N LYS A 316 " pdb=" CA LYS A 316 " pdb=" C LYS A 316 " ideal model delta sigma weight residual 113.23 100.07 13.16 1.24e+00 6.50e-01 1.13e+02 angle pdb=" N ARG B 73 " pdb=" CA ARG B 73 " pdb=" C ARG B 73 " ideal model delta sigma weight residual 112.92 125.37 -12.45 1.23e+00 6.61e-01 1.02e+02 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 111.40 123.14 -11.74 1.22e+00 6.72e-01 9.26e+01 angle pdb=" C CYS C 74 " pdb=" N PRO C 75 " pdb=" CA PRO C 75 " ideal model delta sigma weight residual 119.84 131.79 -11.95 1.25e+00 6.40e-01 9.14e+01 ... (remaining 23299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9294 17.70 - 35.41: 622 35.41 - 53.11: 129 53.11 - 70.81: 21 70.81 - 88.51: 17 Dihedral angle restraints: 10083 sinusoidal: 3880 harmonic: 6203 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -168.58 82.58 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual -86.00 -152.73 66.73 1 1.00e+01 1.00e-02 5.81e+01 ... (remaining 10080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.648: 2640 0.648 - 1.296: 0 1.296 - 1.944: 0 1.944 - 2.592: 0 2.592 - 3.240: 1 Chirality restraints: 2641 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 154 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 0.84 -3.24 2.00e-01 2.50e+01 2.62e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.15e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.04e+01 ... (remaining 2638 not shown) Planarity restraints: 2943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 154 " -0.031 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" CG ASN A 154 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 154 " -0.172 2.00e-02 2.50e+03 pdb=" ND2 ASN A 154 " 0.432 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.305 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 239 " -0.031 2.00e-02 2.50e+03 6.49e-02 4.22e+01 pdb=" C LYS C 239 " 0.112 2.00e-02 2.50e+03 pdb=" O LYS C 239 " -0.043 2.00e-02 2.50e+03 pdb=" N GLU C 240 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 1 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C ILE C 1 " 0.084 2.00e-02 2.50e+03 pdb=" O ILE C 1 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG C 2 " -0.028 2.00e-02 2.50e+03 ... (remaining 2940 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 10 1.67 - 2.47: 180 2.47 - 3.28: 18104 3.28 - 4.09: 39051 4.09 - 4.90: 71646 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128991 Sorted by model distance: nonbonded pdb=" OD2 ASP B 10 " pdb=" NH2 ARG B 420 " model vdw 0.857 2.520 nonbonded pdb=" CD2 TYR l 36 " pdb=" CD2 LEU l 46 " model vdw 1.362 3.760 nonbonded pdb=" O PHE B 312 " pdb=" CD1 ILE B 396 " model vdw 1.364 3.460 nonbonded pdb=" CD2 LEU B 472 " pdb=" CE MET B 487 " model vdw 1.472 3.880 nonbonded pdb=" OG SER h 100J" pdb=" NE ARG C 73 " model vdw 1.517 2.520 ... (remaining 128986 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' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = (chain 'H' and (resid 1 through 100 or resid 100B through 112)) selection = chain 'h' } ncs_group { reference = (chain 'L' and resid 8 through 105) selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.410 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 45.950 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.008 0.105 17196 Z= 0.536 Angle : 0.969 15.659 23304 Z= 0.574 Chirality : 0.086 3.240 2641 Planarity : 0.006 0.099 2942 Dihedral : 12.959 88.515 6081 Min Nonbonded Distance : 0.857 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.57 % Favored : 89.74 % Rotamer: Outliers : 3.00 % Allowed : 9.45 % Favored : 87.55 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % 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: -2.57 (0.16), residues: 2174 helix: -1.25 (0.21), residues: 450 sheet: -0.32 (0.19), residues: 733 loop : -3.08 (0.16), residues: 991 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 457 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 revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 19 residues processed: 497 average time/residue: 0.3051 time to fit residues: 221.0513 Evaluate side-chains 351 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 332 time to evaluate : 1.864 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.1782 time to fit residues: 8.5441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 77 GLN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS A 163 ASN A 288 HIS ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN B 52 ASN B 85 GLN B 134 ASN B 163 ASN B 261 GLN B 344 GLN B 350 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN E 7 HIS C 148 HIS C 154 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS C 350 GLN F 7 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17196 Z= 0.219 Angle : 0.763 18.949 23304 Z= 0.388 Chirality : 0.051 1.012 2641 Planarity : 0.006 0.147 2942 Dihedral : 5.760 30.116 2350 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.89 % Favored : 89.97 % Rotamer: Outliers : 3.22 % Allowed : 15.45 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.17), residues: 2174 helix: 0.17 (0.25), residues: 429 sheet: -0.10 (0.19), residues: 700 loop : -2.69 (0.16), residues: 1045 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 356 time to evaluate : 1.937 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: 58 outliers final: 34 residues processed: 392 average time/residue: 0.2867 time to fit residues: 174.3257 Evaluate side-chains 357 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 323 time to evaluate : 1.944 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1664 time to fit residues: 13.3098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 164 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 40.0000 chunk 213 optimal weight: 3.9990 chunk 175 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 158 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 447 GLN h 35 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17196 Z= 0.396 Angle : 0.779 17.607 23304 Z= 0.403 Chirality : 0.050 0.761 2641 Planarity : 0.005 0.105 2942 Dihedral : 5.760 33.170 2350 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.04 % Favored : 88.82 % Rotamer: Outliers : 3.72 % Allowed : 17.34 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.71 (0.17), residues: 2174 helix: 0.16 (0.26), residues: 429 sheet: 0.08 (0.20), residues: 670 loop : -2.59 (0.16), residues: 1075 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 342 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 37 residues processed: 387 average time/residue: 0.2614 time to fit residues: 158.2846 Evaluate side-chains 351 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 314 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1612 time to fit residues: 13.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 198 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17196 Z= 0.183 Angle : 0.663 12.417 23304 Z= 0.344 Chirality : 0.046 0.701 2641 Planarity : 0.004 0.086 2942 Dihedral : 5.483 31.251 2350 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.03 % Favored : 89.88 % Rotamer: Outliers : 2.56 % Allowed : 18.34 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.47 (0.17), residues: 2174 helix: 0.30 (0.25), residues: 456 sheet: 0.30 (0.21), residues: 655 loop : -2.51 (0.16), residues: 1063 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 330 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 359 average time/residue: 0.2721 time to fit residues: 150.6250 Evaluate side-chains 325 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 300 time to evaluate : 1.914 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1588 time to fit residues: 9.8348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 156 optimal weight: 50.0000 chunk 86 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 144 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS B 226 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17196 Z= 0.483 Angle : 0.806 15.872 23304 Z= 0.417 Chirality : 0.050 0.644 2641 Planarity : 0.005 0.082 2942 Dihedral : 5.767 31.600 2350 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.41 % Favored : 88.45 % Rotamer: Outliers : 3.50 % Allowed : 19.96 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % 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: -1.68 (0.17), residues: 2174 helix: -0.12 (0.25), residues: 459 sheet: 0.18 (0.20), residues: 670 loop : -2.56 (0.17), residues: 1045 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 332 time to evaluate : 1.953 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: 63 outliers final: 41 residues processed: 373 average time/residue: 0.2753 time to fit residues: 158.7417 Evaluate side-chains 357 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 316 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1594 time to fit residues: 14.7778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 50.0000 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 331 GLN B 85 GLN B 148 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17196 Z= 0.335 Angle : 0.719 14.003 23304 Z= 0.371 Chirality : 0.048 0.634 2641 Planarity : 0.005 0.068 2942 Dihedral : 5.625 31.690 2350 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.32 % Favored : 88.50 % Rotamer: Outliers : 2.89 % Allowed : 20.34 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.53 (0.18), residues: 2174 helix: 0.03 (0.25), residues: 462 sheet: 0.17 (0.20), residues: 694 loop : -2.46 (0.17), residues: 1018 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 333 time to evaluate : 1.694 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: 52 outliers final: 29 residues processed: 365 average time/residue: 0.2658 time to fit residues: 149.8431 Evaluate side-chains 347 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 318 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1553 time to fit residues: 10.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 331 GLN A 371 ASN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 148 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17196 Z= 0.272 Angle : 0.686 12.248 23304 Z= 0.355 Chirality : 0.047 0.615 2641 Planarity : 0.004 0.056 2942 Dihedral : 5.496 29.929 2350 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.81 % Favored : 89.01 % Rotamer: Outliers : 1.67 % Allowed : 22.01 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.18), residues: 2174 helix: 0.14 (0.25), residues: 462 sheet: 0.22 (0.20), residues: 736 loop : -2.56 (0.18), residues: 976 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 329 time to evaluate : 2.014 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: 30 outliers final: 18 residues processed: 346 average time/residue: 0.2697 time to fit residues: 144.8081 Evaluate side-chains 337 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 319 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1670 time to fit residues: 8.1171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 344 GLN B 85 GLN B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 39 GLN l 38 GLN C 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17196 Z= 0.174 Angle : 0.642 9.346 23304 Z= 0.332 Chirality : 0.045 0.601 2641 Planarity : 0.004 0.050 2942 Dihedral : 5.332 34.339 2350 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.44 % Favored : 89.42 % Rotamer: Outliers : 0.78 % Allowed : 22.85 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.31 (0.18), residues: 2174 helix: 0.39 (0.26), residues: 456 sheet: 0.23 (0.20), residues: 690 loop : -2.33 (0.17), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 320 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 324 average time/residue: 0.2740 time to fit residues: 137.6920 Evaluate side-chains 314 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 305 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1654 time to fit residues: 5.1738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 172 ASN B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17196 Z= 0.354 Angle : 0.724 10.411 23304 Z= 0.375 Chirality : 0.048 0.575 2641 Planarity : 0.005 0.050 2942 Dihedral : 5.462 33.638 2350 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.32 % Favored : 88.55 % Rotamer: Outliers : 1.11 % Allowed : 23.46 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.39 (0.18), residues: 2174 helix: 0.23 (0.25), residues: 459 sheet: 0.22 (0.20), residues: 738 loop : -2.48 (0.18), residues: 977 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 317 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 328 average time/residue: 0.2819 time to fit residues: 145.3071 Evaluate side-chains 318 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 310 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1536 time to fit residues: 4.8787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17196 Z= 0.175 Angle : 0.648 9.208 23304 Z= 0.335 Chirality : 0.044 0.310 2641 Planarity : 0.004 0.050 2942 Dihedral : 5.265 33.223 2350 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.26 % Favored : 89.60 % Rotamer: Outliers : 0.72 % Allowed : 23.51 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.20 (0.18), residues: 2174 helix: 0.54 (0.26), residues: 456 sheet: 0.32 (0.20), residues: 683 loop : -2.29 (0.17), residues: 1035 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 321 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 326 average time/residue: 0.2735 time to fit residues: 137.2283 Evaluate side-chains 314 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 308 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1655 time to fit residues: 4.4391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 158 optimal weight: 50.0000 chunk 25 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 72 optimal weight: 40.0000 chunk 177 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 151 optimal weight: 50.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS B 148 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.185625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124182 restraints weight = 20084.590| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.23 r_work: 0.3237 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17196 Z= 0.244 Angle : 0.680 12.051 23304 Z= 0.346 Chirality : 0.045 0.285 2641 Planarity : 0.004 0.049 2942 Dihedral : 5.232 32.045 2350 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.35 % Favored : 89.51 % Rotamer: Outliers : 0.11 % Allowed : 24.57 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.18), residues: 2174 helix: 0.52 (0.25), residues: 459 sheet: 0.33 (0.20), residues: 682 loop : -2.26 (0.18), residues: 1033 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3868.10 seconds wall clock time: 70 minutes 56.99 seconds (4256.99 seconds total)