Starting phenix.real_space_refine (version: dev) on Tue Apr 5 05:46:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxw_20523/04_2022/6pxw_20523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxw_20523/04_2022/6pxw_20523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxw_20523/04_2022/6pxw_20523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxw_20523/04_2022/6pxw_20523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxw_20523/04_2022/6pxw_20523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxw_20523/04_2022/6pxw_20523.pdb" } resolution = 3.1 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 11198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4876 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 28, 'TRANS': 571, 'PCIS': 1} Chain breaks: 4 Chain: "B" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4876 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 28, 'TRANS': 571, 'PCIS': 1} Chain breaks: 4 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "E" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "F" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Time building chain proxies: 6.79, per 1000 atoms: 0.61 Number of scatterers: 11198 At special positions: 0 Unit cell: (129.47, 129.47, 87.74, 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 106 16.00 O 2064 8.00 N 1912 7.00 C 7116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.02 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.02 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.02 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.04 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.02 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 22 sheets defined 21.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.904A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.849A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.758A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.666A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.059A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.610A pdb=" N SER A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.904A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.850A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.757A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.665A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 4.060A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 692 through 714 removed outlier: 3.611A pdb=" N SER B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 703 " --> pdb=" O SER B 699 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 714 " --> pdb=" O HIS B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 67 through 73 removed outlier: 3.640A pdb=" N LEU F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 removed outlier: 6.864A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.388A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.585A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE A 534 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 64 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR B 172 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AB7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.863A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC1, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.389A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC3, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.585A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE B 534 " --> pdb=" O PHE B 503 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 600 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: 3.49 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3533 1.34 - 1.46: 2575 1.46 - 1.58: 5226 1.58 - 1.70: 0 1.70 - 1.83: 124 Bond restraints: 11458 Sorted by residual: bond pdb=" C ILE B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.30e-02 5.92e+03 4.97e+00 bond pdb=" C ILE A 285 " pdb=" N PRO A 286 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.30e-02 5.92e+03 4.63e+00 bond pdb=" CG1 ILE A 95 " pdb=" CD1 ILE A 95 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CG1 ILE B 95 " pdb=" CD1 ILE B 95 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CB VAL B 179 " pdb=" CG2 VAL B 179 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 ... (remaining 11453 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.34: 334 106.34 - 113.28: 6058 113.28 - 120.23: 4290 120.23 - 127.17: 4679 127.17 - 134.12: 149 Bond angle restraints: 15510 Sorted by residual: angle pdb=" C THR B 578 " pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" N HIS F 10 " pdb=" CA HIS F 10 " pdb=" C HIS F 10 " ideal model delta sigma weight residual 111.07 104.96 6.11 1.07e+00 8.73e-01 3.26e+01 angle pdb=" N HIS E 10 " pdb=" CA HIS E 10 " pdb=" C HIS E 10 " ideal model delta sigma weight residual 111.07 105.19 5.88 1.07e+00 8.73e-01 3.02e+01 angle pdb=" C GLU B 469 " pdb=" N ASN B 470 " pdb=" CA ASN B 470 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C GLU A 469 " pdb=" N ASN A 470 " pdb=" CA ASN A 470 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 ... (remaining 15505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.02: 6224 12.02 - 24.04: 550 24.04 - 36.06: 101 36.06 - 48.08: 43 48.08 - 60.10: 26 Dihedral angle restraints: 6944 sinusoidal: 2902 harmonic: 4042 Sorted by residual: dihedral pdb=" CA THR B 578 " pdb=" C THR B 578 " pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta harmonic sigma weight residual 180.00 137.11 42.89 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.03 -56.03 1 1.00e+01 1.00e-02 4.24e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1186 0.056 - 0.112: 383 0.112 - 0.168: 106 0.168 - 0.224: 9 0.224 - 0.279: 8 Chirality restraints: 1692 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE A 395 " pdb=" CA ILE A 395 " pdb=" CG1 ILE A 395 " pdb=" CG2 ILE A 395 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1689 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 578 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C THR B 578 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 578 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR B 579 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 542 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A 543 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 542 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO B 543 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.036 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2474 2.78 - 3.31: 9097 3.31 - 3.84: 17401 3.84 - 4.37: 20428 4.37 - 4.90: 36084 Nonbonded interactions: 85484 Sorted by model distance: nonbonded pdb=" OE2 GLU A 698 " pdb=" OH TYR B 144 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU B 698 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.295 2.440 nonbonded pdb=" OE2 GLU B 355 " pdb=" NH2 ARG B 383 " model vdw 2.334 2.520 ... (remaining 85479 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' } ncs_group { reference = (chain 'C' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'D' and (resid 4 through 26 or resid 56 through 76)) 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 106 5.16 5 C 7116 2.51 5 N 1912 2.21 5 O 2064 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 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.600 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 31.940 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 0.074 11458 Z= 0.555 Angle : 0.992 11.238 15510 Z= 0.555 Chirality : 0.060 0.279 1692 Planarity : 0.007 0.066 1994 Dihedral : 9.829 58.761 4216 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.85 % Favored : 89.63 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.04 (0.18), residues: 1350 helix: -3.24 (0.25), residues: 224 sheet: -2.94 (0.28), residues: 174 loop : -2.66 (0.17), residues: 952 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 215 average time/residue: 0.3172 time to fit residues: 89.4586 Evaluate side-chains 104 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0994 time to fit residues: 2.2176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 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 15 ASN A 32 HIS A 100 HIS A 175 ASN A 209 HIS A 247 HIS A 276 GLN A 328 GLN A 357 ASN A 405 ASN A 407 ASN A 541 ASN A 546 GLN A 561 GLN B 15 ASN B 32 HIS B 100 HIS B 175 ASN B 209 HIS B 247 HIS B 276 GLN B 328 GLN B 405 ASN B 407 ASN B 429 HIS B 546 GLN B 561 GLN D 70 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11458 Z= 0.185 Angle : 0.598 7.613 15510 Z= 0.316 Chirality : 0.045 0.204 1692 Planarity : 0.004 0.052 1994 Dihedral : 5.922 32.300 1506 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.20), residues: 1350 helix: -2.05 (0.29), residues: 252 sheet: -2.21 (0.35), residues: 140 loop : -2.46 (0.18), residues: 958 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.385 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 112 average time/residue: 0.2465 time to fit residues: 39.5004 Evaluate side-chains 90 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0984 time to fit residues: 2.4005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.4980 chunk 133 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 429 HIS A 546 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 11458 Z= 0.299 Angle : 0.619 8.387 15510 Z= 0.324 Chirality : 0.046 0.145 1692 Planarity : 0.004 0.049 1994 Dihedral : 5.664 32.029 1506 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.56 % Favored : 90.37 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.99 (0.21), residues: 1350 helix: -1.50 (0.31), residues: 252 sheet: -2.02 (0.37), residues: 140 loop : -2.27 (0.19), residues: 958 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.452 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 100 average time/residue: 0.2397 time to fit residues: 35.2845 Evaluate side-chains 82 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1401 time to fit residues: 3.6286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 513 GLN A 546 GLN A 561 GLN B 295 ASN B 513 GLN B 546 GLN B 561 GLN F 70 GLN F 73 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11458 Z= 0.228 Angle : 0.565 7.187 15510 Z= 0.298 Chirality : 0.044 0.136 1692 Planarity : 0.004 0.045 1994 Dihedral : 5.370 31.575 1506 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.48 % Favored : 92.44 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.73 (0.22), residues: 1350 helix: -1.20 (0.32), residues: 248 sheet: -1.87 (0.39), residues: 140 loop : -2.11 (0.19), residues: 962 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 95 average time/residue: 0.2876 time to fit residues: 38.2932 Evaluate side-chains 81 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1022 time to fit residues: 2.3085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 561 GLN B 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 11458 Z= 0.146 Angle : 0.507 7.024 15510 Z= 0.269 Chirality : 0.042 0.139 1692 Planarity : 0.003 0.043 1994 Dihedral : 4.994 31.325 1506 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.44 (0.22), residues: 1350 helix: -0.91 (0.32), residues: 248 sheet: -1.84 (0.42), residues: 130 loop : -1.91 (0.20), residues: 972 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.354 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 103 average time/residue: 0.2467 time to fit residues: 36.6721 Evaluate side-chains 87 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0967 time to fit residues: 2.0997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 561 GLN B 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11458 Z= 0.295 Angle : 0.584 7.296 15510 Z= 0.306 Chirality : 0.045 0.144 1692 Planarity : 0.004 0.041 1994 Dihedral : 5.155 31.072 1506 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.15 % Favored : 89.78 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.22), residues: 1350 helix: -0.91 (0.33), residues: 248 sheet: -1.85 (0.42), residues: 130 loop : -1.90 (0.20), residues: 972 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.469 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 0.2584 time to fit residues: 34.3590 Evaluate side-chains 83 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1485 time to fit residues: 3.6002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN B 185 HIS B 546 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11458 Z= 0.214 Angle : 0.542 7.071 15510 Z= 0.286 Chirality : 0.043 0.135 1692 Planarity : 0.003 0.040 1994 Dihedral : 5.059 31.534 1506 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.67 % Favored : 91.26 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.33 (0.22), residues: 1350 helix: -0.77 (0.33), residues: 248 sheet: -1.84 (0.42), residues: 130 loop : -1.84 (0.20), residues: 972 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.367 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 88 average time/residue: 0.2545 time to fit residues: 32.7006 Evaluate side-chains 78 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1163 time to fit residues: 2.0548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 11458 Z= 0.132 Angle : 0.497 6.765 15510 Z= 0.262 Chirality : 0.042 0.135 1692 Planarity : 0.003 0.043 1994 Dihedral : 4.691 31.190 1506 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.15 (0.22), residues: 1350 helix: -0.54 (0.33), residues: 248 sheet: -1.79 (0.43), residues: 130 loop : -1.73 (0.20), residues: 972 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.260 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 88 average time/residue: 0.2441 time to fit residues: 31.6289 Evaluate side-chains 82 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1117 time to fit residues: 2.7120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 276 GLN A 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11458 Z= 0.224 Angle : 0.540 7.271 15510 Z= 0.282 Chirality : 0.043 0.134 1692 Planarity : 0.003 0.040 1994 Dihedral : 4.792 30.877 1506 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.17 (0.22), residues: 1350 helix: -0.49 (0.33), residues: 248 sheet: -1.81 (0.43), residues: 130 loop : -1.76 (0.20), residues: 972 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.430 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 84 average time/residue: 0.2417 time to fit residues: 29.9173 Evaluate side-chains 78 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1146 time to fit residues: 2.1839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 0.0030 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 11458 Z= 0.153 Angle : 0.511 7.240 15510 Z= 0.267 Chirality : 0.043 0.134 1692 Planarity : 0.003 0.041 1994 Dihedral : 4.675 30.801 1506 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.09 (0.22), residues: 1350 helix: -0.40 (0.33), residues: 248 sheet: -1.78 (0.43), residues: 130 loop : -1.70 (0.20), residues: 972 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.391 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.2658 time to fit residues: 32.0963 Evaluate side-chains 81 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1030 time to fit residues: 2.1705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 110 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 452 GLN A 546 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.121343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094507 restraints weight = 18696.199| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.69 r_work: 0.3323 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3301 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work: 0.3290 rms_B_bonded: 2.51 restraints_weight: 0.0625 r_work: 0.3278 rms_B_bonded: 2.59 restraints_weight: 0.0312 r_work: 0.3265 rms_B_bonded: 2.71 restraints_weight: 0.0156 r_work: 0.3252 rms_B_bonded: 2.84 restraints_weight: 0.0078 r_work: 0.3239 rms_B_bonded: 3.00 restraints_weight: 0.0039 r_work: 0.3225 rms_B_bonded: 3.19 restraints_weight: 0.0020 r_work: 0.3209 rms_B_bonded: 3.41 restraints_weight: 0.0010 r_work: 0.3193 rms_B_bonded: 3.66 restraints_weight: 0.0005 r_work: 0.3176 rms_B_bonded: 3.95 restraints_weight: 0.0002 r_work: 0.3158 rms_B_bonded: 4.27 restraints_weight: 0.0001 r_work: 0.3138 rms_B_bonded: 4.63 restraints_weight: 0.0001 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 11458 Z= 0.122 Angle : 0.492 7.226 15510 Z= 0.257 Chirality : 0.042 0.150 1692 Planarity : 0.003 0.043 1994 Dihedral : 4.454 30.321 1506 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.96 (0.23), residues: 1350 helix: -0.28 (0.33), residues: 248 sheet: -1.88 (0.45), residues: 120 loop : -1.60 (0.20), residues: 982 =============================================================================== Job complete usr+sys time: 2106.61 seconds wall clock time: 39 minutes 4.52 seconds (2344.52 seconds total)