Starting phenix.real_space_refine (version: dev) on Wed Feb 22 05:04:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/02_2023/7lft_23306_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/02_2023/7lft_23306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/02_2023/7lft_23306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/02_2023/7lft_23306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/02_2023/7lft_23306_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lft_23306/02_2023/7lft_23306_trim_updated.pdb" } resolution = 2.6 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 Process input model Symmetric amino acids flipped Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A ARG 478": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C GLU 464": "OE1" <-> "OE2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D ARG 560": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15479 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "D" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {' K': 3, 'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.93, per 1000 atoms: 0.58 Number of scatterers: 15479 At special positions: 0 Unit cell: (95.372, 95.372, 119.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 76 16.00 P 8 15.00 O 2732 8.00 N 2380 7.00 C 10280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 62.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.210A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 403 Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 456 removed outlier: 4.684A pdb=" N TYR A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 removed outlier: 4.515A pdb=" N ASP A 482 " --> pdb=" O ILE A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 604 Processing helix chain 'B' and resid 163 through 188 Proline residue: B 175 - end of helix removed outlier: 5.210A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 325 Processing helix chain 'B' and resid 345 through 360 Processing helix chain 'B' and resid 372 through 403 Processing helix chain 'B' and resid 405 through 423 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 450 through 456 removed outlier: 4.683A pdb=" N TYR B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 482 removed outlier: 4.515A pdb=" N ASP B 482 " --> pdb=" O ILE B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 604 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 5.210A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 405 through 423 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 4.683A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 482 removed outlier: 4.516A pdb=" N ASP C 482 " --> pdb=" O ILE C 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 604 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 175 - end of helix removed outlier: 5.210A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 253 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 268 through 289 removed outlier: 4.034A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 403 Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 4.683A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 476 removed outlier: 6.118A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 482 removed outlier: 4.515A pdb=" N ASP D 482 " --> pdb=" O ILE D 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.691A pdb=" N LYS D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 removed outlier: 4.828A pdb=" N GLU D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 604 Processing sheet with id= A, first strand: chain 'A' and resid 496 through 498 Processing sheet with id= B, first strand: chain 'A' and resid 564 through 567 removed outlier: 3.880A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 496 through 498 Processing sheet with id= D, first strand: chain 'B' and resid 564 through 567 removed outlier: 3.880A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 496 through 498 Processing sheet with id= F, first strand: chain 'C' and resid 564 through 567 removed outlier: 3.879A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 496 through 498 Processing sheet with id= H, first strand: chain 'D' and resid 564 through 567 removed outlier: 3.880A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2292 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: 4.26 Time building geometry restraints manager: 6.94 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: 2376 1.27 - 1.41: 3932 1.41 - 1.54: 9096 1.54 - 1.67: 280 1.67 - 1.80: 128 Bond restraints: 15812 Sorted by residual: bond pdb=" C VAL D 370 " pdb=" O VAL D 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL A 370 " pdb=" O VAL A 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL B 370 " pdb=" O VAL B 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL C 370 " pdb=" O VAL C 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.98e+01 bond pdb=" C31 CPL D 706 " pdb=" O2 CPL D 706 " ideal model delta sigma weight residual 1.332 1.434 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 15807 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.12: 273 105.12 - 112.38: 8331 112.38 - 119.63: 5078 119.63 - 126.88: 7474 126.88 - 134.14: 172 Bond angle restraints: 21328 Sorted by residual: angle pdb=" O3P CPL A 707 " pdb=" P CPL A 707 " pdb=" O4P CPL A 707 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL D 706 " pdb=" P CPL D 706 " pdb=" O4P CPL D 706 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL C 706 " pdb=" P CPL C 706 " pdb=" O4P CPL C 706 " ideal model delta sigma weight residual 93.29 116.17 -22.88 3.00e+00 1.11e-01 5.82e+01 angle pdb=" O3P CPL B 706 " pdb=" P CPL B 706 " pdb=" O4P CPL B 706 " ideal model delta sigma weight residual 93.29 116.12 -22.83 3.00e+00 1.11e-01 5.79e+01 angle pdb=" N VAL A 370 " pdb=" CA VAL A 370 " pdb=" C VAL A 370 " ideal model delta sigma weight residual 111.56 106.32 5.24 8.60e-01 1.35e+00 3.71e+01 ... (remaining 21323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 8367 17.27 - 34.54: 773 34.54 - 51.81: 168 51.81 - 69.08: 68 69.08 - 86.35: 12 Dihedral angle restraints: 9388 sinusoidal: 4064 harmonic: 5324 Sorted by residual: dihedral pdb=" CA VAL C 469 " pdb=" C VAL C 469 " pdb=" N HIS C 470 " pdb=" CA HIS C 470 " ideal model delta harmonic sigma weight residual 180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA VAL B 469 " pdb=" C VAL B 469 " pdb=" N HIS B 470 " pdb=" CA HIS B 470 " ideal model delta harmonic sigma weight residual 180.00 -163.66 -16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA VAL A 469 " pdb=" C VAL A 469 " pdb=" N HIS A 470 " pdb=" CA HIS A 470 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 9385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2238 0.094 - 0.188: 93 0.188 - 0.282: 29 0.282 - 0.377: 0 0.377 - 0.471: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" C10 CLR A 702 " pdb=" C1 CLR A 702 " pdb=" C5 CLR A 702 " pdb=" C9 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C10 CLR C 701 " pdb=" C1 CLR C 701 " pdb=" C5 CLR C 701 " pdb=" C9 CLR C 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C10 CLR D 701 " pdb=" C1 CLR D 701 " pdb=" C5 CLR D 701 " pdb=" C9 CLR D 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2365 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 501 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO D 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 501 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 502 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 501 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.020 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.49: 69 2.49 - 3.16: 13283 3.16 - 3.82: 32568 3.82 - 4.48: 46112 4.48 - 5.14: 71641 Nonbonded interactions: 163673 Sorted by model distance: nonbonded pdb=" K K A 710 " pdb=" K K A 711 " model vdw 1.832 2.660 nonbonded pdb=" OG SER A 567 " pdb=" OG SER A 571 " model vdw 2.187 2.440 nonbonded pdb=" OG SER D 567 " pdb=" OG SER D 571 " model vdw 2.188 2.440 nonbonded pdb=" OG SER C 567 " pdb=" OG SER C 571 " model vdw 2.188 2.440 nonbonded pdb=" OG SER B 567 " pdb=" OG SER B 571 " model vdw 2.188 2.440 ... (remaining 163668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 605 or resid 701 through 708)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 8 5.49 5 S 76 5.16 5 C 10280 2.51 5 N 2380 2.21 5 O 2732 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: 0.930 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: 6.520 Check model and map are aligned: 0.210 Process input model: 40.350 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 : 0.009 0.102 15812 Z= 0.588 Angle : 1.096 22.901 21328 Z= 0.478 Chirality : 0.057 0.471 2368 Planarity : 0.004 0.036 2552 Dihedral : 14.799 86.350 5972 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.25 % 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: -0.82 (0.18), residues: 1792 helix: -0.10 (0.14), residues: 1176 sheet: -2.84 (1.00), residues: 20 loop : -1.13 (0.23), residues: 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 1.944 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 1.4890 time to fit residues: 376.9091 Evaluate side-chains 168 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.0040 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 470 HIS A 534 GLN A 559 ASN B 226 GLN B 470 HIS B 534 GLN B 559 ASN C 226 GLN C 470 HIS C 534 GLN C 559 ASN D 226 GLN D 470 HIS D 534 GLN D 559 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15812 Z= 0.155 Angle : 0.450 8.147 21328 Z= 0.240 Chirality : 0.038 0.142 2368 Planarity : 0.004 0.032 2552 Dihedral : 11.588 81.613 2392 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.42 % 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: 0.54 (0.19), residues: 1792 helix: 0.98 (0.14), residues: 1200 sheet: -2.62 (0.97), residues: 20 loop : -0.73 (0.25), residues: 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 1.985 Fit side-chains outliers start: 23 outliers final: 0 residues processed: 208 average time/residue: 1.2769 time to fit residues: 293.5743 Evaluate side-chains 164 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 419 GLN A 551 ASN B 226 GLN B 419 GLN B 551 ASN C 419 GLN C 551 ASN D 226 GLN D 419 GLN D 551 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 15812 Z= 0.355 Angle : 0.561 5.714 21328 Z= 0.297 Chirality : 0.043 0.144 2368 Planarity : 0.004 0.036 2552 Dihedral : 11.036 81.891 2392 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 2.09 % 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: 0.69 (0.19), residues: 1792 helix: 1.05 (0.15), residues: 1200 sheet: -2.87 (0.90), residues: 20 loop : -0.57 (0.25), residues: 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.803 Fit side-chains outliers start: 34 outliers final: 8 residues processed: 192 average time/residue: 1.4204 time to fit residues: 299.9337 Evaluate side-chains 164 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 329 ASN C 329 ASN D 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 15812 Z= 0.152 Angle : 0.432 5.205 21328 Z= 0.232 Chirality : 0.038 0.147 2368 Planarity : 0.003 0.033 2552 Dihedral : 9.387 77.893 2392 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.59 % 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: 1.18 (0.20), residues: 1792 helix: 1.44 (0.15), residues: 1204 sheet: -2.57 (0.93), residues: 20 loop : -0.40 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.776 Fit side-chains outliers start: 42 outliers final: 12 residues processed: 202 average time/residue: 1.4327 time to fit residues: 316.7297 Evaluate side-chains 165 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.6636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 156 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15812 Z= 0.205 Angle : 0.467 5.287 21328 Z= 0.250 Chirality : 0.038 0.144 2368 Planarity : 0.003 0.032 2552 Dihedral : 9.234 73.696 2392 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 3.08 % 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: 1.30 (0.20), residues: 1792 helix: 1.50 (0.15), residues: 1204 sheet: -2.62 (0.90), residues: 20 loop : -0.29 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 161 time to evaluate : 2.111 Fit side-chains outliers start: 50 outliers final: 15 residues processed: 203 average time/residue: 1.3866 time to fit residues: 309.6052 Evaluate side-chains 168 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 2.3744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 329 ASN C 329 ASN D 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15812 Z= 0.190 Angle : 0.464 5.250 21328 Z= 0.248 Chirality : 0.038 0.148 2368 Planarity : 0.003 0.033 2552 Dihedral : 8.794 71.155 2392 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 2.46 % 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: 1.42 (0.20), residues: 1792 helix: 1.60 (0.15), residues: 1204 sheet: -2.68 (0.87), residues: 20 loop : -0.24 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 1.800 Fit side-chains outliers start: 40 outliers final: 22 residues processed: 193 average time/residue: 1.3267 time to fit residues: 284.7127 Evaluate side-chains 169 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 2.4133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 15812 Z= 0.257 Angle : 0.510 5.391 21328 Z= 0.271 Chirality : 0.040 0.145 2368 Planarity : 0.004 0.033 2552 Dihedral : 9.177 71.815 2392 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.65 % 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: 1.35 (0.20), residues: 1792 helix: 1.54 (0.15), residues: 1200 sheet: -2.89 (0.83), residues: 20 loop : -0.25 (0.26), residues: 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.933 Fit side-chains outliers start: 43 outliers final: 28 residues processed: 188 average time/residue: 1.2751 time to fit residues: 265.9913 Evaluate side-chains 174 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.6185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 329 ASN C 329 ASN D 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15812 Z= 0.210 Angle : 0.490 8.672 21328 Z= 0.258 Chirality : 0.039 0.147 2368 Planarity : 0.004 0.034 2552 Dihedral : 8.706 71.194 2392 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 2.40 % 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: 1.40 (0.20), residues: 1792 helix: 1.60 (0.15), residues: 1200 sheet: -2.99 (0.80), residues: 20 loop : -0.29 (0.26), residues: 572 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 1.872 Fit side-chains outliers start: 39 outliers final: 26 residues processed: 193 average time/residue: 1.3691 time to fit residues: 291.1492 Evaluate side-chains 174 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 2.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.0370 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15812 Z= 0.182 Angle : 0.477 8.119 21328 Z= 0.252 Chirality : 0.038 0.144 2368 Planarity : 0.003 0.034 2552 Dihedral : 8.228 69.802 2392 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.34 % 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 (0.20), residues: 1792 helix: 1.62 (0.15), residues: 1204 sheet: -3.03 (0.78), residues: 20 loop : -0.21 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.777 Fit side-chains outliers start: 38 outliers final: 24 residues processed: 187 average time/residue: 1.3332 time to fit residues: 275.5948 Evaluate side-chains 172 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 2.5743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.0770 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 329 ASN C 329 ASN D 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 15812 Z= 0.136 Angle : 0.446 8.132 21328 Z= 0.235 Chirality : 0.037 0.144 2368 Planarity : 0.003 0.035 2552 Dihedral : 7.435 64.936 2392 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 1.91 % 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: 1.63 (0.20), residues: 1792 helix: 1.74 (0.15), residues: 1204 sheet: -2.72 (0.82), residues: 20 loop : -0.12 (0.27), residues: 568 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.786 Fit side-chains outliers start: 31 outliers final: 21 residues processed: 192 average time/residue: 1.3768 time to fit residues: 292.0690 Evaluate side-chains 164 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 2.3077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 21 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 534 GLN B 329 ASN B 534 GLN C 329 ASN C 534 GLN D 329 ASN D 534 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108184 restraints weight = 17810.739| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.13 r_work: 0.3103 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 15812 Z= 0.141 Angle : 0.446 7.988 21328 Z= 0.234 Chirality : 0.037 0.142 2368 Planarity : 0.003 0.035 2552 Dihedral : 7.303 60.729 2392 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.60 % 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: 1.69 (0.20), residues: 1792 helix: 1.76 (0.15), residues: 1204 sheet: -2.43 (0.87), residues: 20 loop : -0.03 (0.27), residues: 568 =============================================================================== Job complete usr+sys time: 5199.76 seconds wall clock time: 93 minutes 21.42 seconds (5601.42 seconds total)