Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 13:02:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/04_2023/6vqt_21356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/04_2023/6vqt_21356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/04_2023/6vqt_21356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/04_2023/6vqt_21356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/04_2023/6vqt_21356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/04_2023/6vqt_21356_updated.pdb" } resolution = 3.03 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 657 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 5822 2.51 5 N 1620 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 31": "OD1" <-> "OD2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A ASP 535": "OD1" <-> "OD2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B ARG 494": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ASP 586": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9144 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4539 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 15, 'TRANS': 568} Chain: "B" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4539 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 15, 'TRANS': 568} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.23, per 1000 atoms: 0.57 Number of scatterers: 9144 At special positions: 0 Unit cell: (72.437, 91.1854, 141.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 24 16.00 P 4 15.00 Mg 2 11.99 O 1670 8.00 N 1620 7.00 C 5822 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 66.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 33 through 67 removed outlier: 3.835A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 79 through 126 removed outlier: 5.040A pdb=" N ARG A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.568A pdb=" N LEU A 133 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 183 through 236 removed outlier: 4.335A pdb=" N HIS A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 293 removed outlier: 3.846A pdb=" N ALA A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 316 Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 322 through 340 Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.577A pdb=" N ALA A 404 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.614A pdb=" N GLY A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 473 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'A' and resid 556 through 559 Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 588 through 597 Processing helix chain 'B' and resid 16 through 27 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 34 through 67 Proline residue: B 57 - end of helix removed outlier: 3.507A pdb=" N MET B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 126 removed outlier: 3.503A pdb=" N VAL B 95 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.751A pdb=" N ALA B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 160 Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 183 through 236 removed outlier: 4.103A pdb=" N HIS B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 293 removed outlier: 3.771A pdb=" N ALA B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.720A pdb=" N ARG B 313 " --> pdb=" O GLN B 310 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.710A pdb=" N MET B 317 " --> pdb=" O PRO B 314 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 340 Processing helix chain 'B' and resid 400 through 407 removed outlier: 4.124A pdb=" N ALA B 404 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 451 through 458 removed outlier: 4.598A pdb=" N GLY B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 500 through 514 Processing helix chain 'B' and resid 530 through 544 Processing helix chain 'B' and resid 556 through 559 Processing helix chain 'B' and resid 579 through 585 Processing helix chain 'B' and resid 588 through 597 Processing sheet with id= A, first strand: chain 'A' and resid 382 through 384 Processing sheet with id= B, first strand: chain 'A' and resid 572 through 577 removed outlier: 7.182A pdb=" N VAL A 567 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 565 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A 549 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 392 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 551 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 382 through 384 Processing sheet with id= D, first strand: chain 'B' and resid 572 through 577 removed outlier: 7.244A pdb=" N VAL B 567 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN B 576 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE B 565 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR B 549 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 392 " --> pdb=" O THR B 549 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER B 551 " --> pdb=" O ILE B 392 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1686 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: 2.79 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3021 1.34 - 1.46: 1165 1.46 - 1.57: 5062 1.57 - 1.69: 8 1.69 - 1.80: 56 Bond restraints: 9312 Sorted by residual: bond pdb=" C1' ADP B 701 " pdb=" C2' ADP B 701 " ideal model delta sigma weight residual 1.524 1.293 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' ADP A 701 " pdb=" C2' ADP A 701 " ideal model delta sigma weight residual 1.524 1.293 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C1' ADP A 701 " pdb=" O4' ADP A 701 " ideal model delta sigma weight residual 1.426 1.624 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C1' ADP B 701 " pdb=" O4' ADP B 701 " ideal model delta sigma weight residual 1.426 1.623 -0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.335 0.155 2.00e-02 2.50e+03 6.01e+01 ... (remaining 9307 not shown) Histogram of bond angle deviations from ideal: 94.09 - 103.36: 80 103.36 - 112.63: 4976 112.63 - 121.90: 5955 121.90 - 131.17: 1616 131.17 - 140.44: 35 Bond angle restraints: 12662 Sorted by residual: angle pdb=" N VAL B 321 " pdb=" CA VAL B 321 " pdb=" C VAL B 321 " ideal model delta sigma weight residual 113.20 105.73 7.47 9.60e-01 1.09e+00 6.05e+01 angle pdb=" O2 VO4 A 702 " pdb=" V VO4 A 702 " pdb=" O4 VO4 A 702 " ideal model delta sigma weight residual 109.47 126.26 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O3 VO4 A 702 " pdb=" V VO4 A 702 " pdb=" O4 VO4 A 702 " ideal model delta sigma weight residual 109.47 126.16 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3 VO4 A 704 " pdb=" V VO4 A 704 " pdb=" O4 VO4 A 704 " ideal model delta sigma weight residual 109.47 126.07 -16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O2 VO4 A 704 " pdb=" V VO4 A 704 " pdb=" O4 VO4 A 704 " ideal model delta sigma weight residual 109.47 125.57 -16.10 3.00e+00 1.11e-01 2.88e+01 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 5270 30.78 - 61.57: 216 61.57 - 92.35: 21 92.35 - 123.14: 1 123.14 - 153.92: 2 Dihedral angle restraints: 5510 sinusoidal: 2144 harmonic: 3366 Sorted by residual: dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 93.92 -153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 170.92 129.07 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 62.49 -122.49 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 5507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 1480 0.187 - 0.375: 2 0.375 - 0.562: 0 0.562 - 0.749: 0 0.749 - 0.936: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" V VO4 A 704 " pdb=" O1 VO4 A 704 " pdb=" O2 VO4 A 704 " pdb=" O4 VO4 A 704 " both_signs ideal model delta sigma weight residual True 5.36 -4.43 0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" V VO4 A 702 " pdb=" O1 VO4 A 702 " pdb=" O2 VO4 A 702 " pdb=" O4 VO4 A 702 " both_signs ideal model delta sigma weight residual True 5.36 4.44 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CG LEU B 582 " pdb=" CB LEU B 582 " pdb=" CD1 LEU B 582 " pdb=" CD2 LEU B 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1481 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 74 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO B 75 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 401 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C SER A 401 " -0.051 2.00e-02 2.50e+03 pdb=" O SER A 401 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 402 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 313 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO B 314 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 314 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 314 " 0.037 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 23 2.37 - 3.00: 5305 3.00 - 3.63: 13354 3.63 - 4.27: 18543 4.27 - 4.90: 30410 Nonbonded interactions: 67635 Sorted by model distance: nonbonded pdb=" V VO4 A 704 " pdb="MG MG B 702 " model vdw 1.733 2.180 nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 702 " model vdw 1.891 2.170 nonbonded pdb=" O4 VO4 A 704 " pdb="MG MG B 702 " model vdw 1.895 2.170 nonbonded pdb=" O3B ADP A 701 " pdb="MG MG A 703 " model vdw 1.920 2.170 nonbonded pdb=" O2 VO4 A 704 " pdb="MG MG B 702 " model vdw 1.969 2.170 ... (remaining 67630 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 15 through 598 or resid 701)) selection = (chain 'B' and (resid 15 through 598 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 6.400 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.940 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 0.231 9312 Z= 0.623 Angle : 1.151 16.795 12662 Z= 0.653 Chirality : 0.061 0.936 1484 Planarity : 0.006 0.080 1602 Dihedral : 16.315 153.919 3346 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 4.94 % 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: 1.39 (0.23), residues: 1164 helix: 1.65 (0.16), residues: 760 sheet: 0.63 (0.54), residues: 78 loop : -0.68 (0.34), residues: 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 115 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 18 residues processed: 158 average time/residue: 0.2458 time to fit residues: 51.8531 Evaluate side-chains 97 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1056 time to fit residues: 4.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 32 ASN A 208 HIS A 263 ASN A 293 GLN A 442 GLN A 570 GLN B 18 GLN B 74 GLN B 102 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 423 GLN B 442 GLN B 504 GLN B 570 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9312 Z= 0.219 Angle : 0.669 10.409 12662 Z= 0.347 Chirality : 0.041 0.162 1484 Planarity : 0.005 0.057 1602 Dihedral : 6.699 107.258 1318 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.82 % 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: 2.56 (0.24), residues: 1164 helix: 2.61 (0.17), residues: 760 sheet: 0.82 (0.50), residues: 78 loop : -0.32 (0.34), residues: 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.2131 time to fit residues: 29.0598 Evaluate side-chains 87 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0861 time to fit residues: 3.1300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 102 ASN B 99 ASN B 161 ASN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9312 Z= 0.186 Angle : 0.607 9.957 12662 Z= 0.309 Chirality : 0.039 0.147 1484 Planarity : 0.004 0.049 1602 Dihedral : 5.977 103.418 1318 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.15 % 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: 2.76 (0.24), residues: 1164 helix: 2.77 (0.18), residues: 754 sheet: 0.84 (0.49), residues: 78 loop : -0.20 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.013 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 104 average time/residue: 0.1793 time to fit residues: 28.2314 Evaluate side-chains 88 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0881 time to fit residues: 3.0593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 99 ASN B 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9312 Z= 0.196 Angle : 0.596 10.908 12662 Z= 0.301 Chirality : 0.039 0.137 1484 Planarity : 0.004 0.048 1602 Dihedral : 5.639 98.097 1318 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 2.04 % 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: 2.78 (0.24), residues: 1164 helix: 2.73 (0.18), residues: 756 sheet: 0.85 (0.51), residues: 78 loop : -0.04 (0.34), residues: 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.142 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 93 average time/residue: 0.1781 time to fit residues: 25.4949 Evaluate side-chains 90 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1251 time to fit residues: 3.9827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.0060 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.0050 chunk 95 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9312 Z= 0.167 Angle : 0.585 10.180 12662 Z= 0.289 Chirality : 0.038 0.141 1484 Planarity : 0.004 0.046 1602 Dihedral : 5.354 95.080 1318 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.18 % 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: 2.79 (0.25), residues: 1164 helix: 2.74 (0.18), residues: 756 sheet: 0.92 (0.52), residues: 78 loop : -0.05 (0.34), residues: 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.081 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 91 average time/residue: 0.1729 time to fit residues: 24.3744 Evaluate side-chains 85 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0999 time to fit residues: 2.2938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.0370 chunk 100 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.0170 overall best weight: 2.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 179 ASN A 214 ASN A 277 ASN A 293 GLN A 504 GLN B 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9312 Z= 0.266 Angle : 0.648 11.309 12662 Z= 0.326 Chirality : 0.039 0.144 1484 Planarity : 0.004 0.043 1602 Dihedral : 5.491 97.755 1318 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.61 % 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: 2.60 (0.25), residues: 1164 helix: 2.65 (0.18), residues: 752 sheet: 0.68 (0.52), residues: 80 loop : -0.20 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.133 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 95 average time/residue: 0.1624 time to fit residues: 24.3984 Evaluate side-chains 86 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0879 time to fit residues: 3.0849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS B 208 HIS B 293 GLN B 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.085 9312 Z= 0.392 Angle : 0.743 10.379 12662 Z= 0.384 Chirality : 0.042 0.154 1484 Planarity : 0.005 0.065 1602 Dihedral : 5.745 87.182 1318 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.93 % 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: 2.00 (0.24), residues: 1164 helix: 2.13 (0.18), residues: 756 sheet: 0.37 (0.54), residues: 80 loop : -0.29 (0.35), residues: 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.132 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.1787 time to fit residues: 25.6838 Evaluate side-chains 91 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1464 time to fit residues: 3.9889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 293 GLN B 125 HIS B 208 HIS B 293 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9312 Z= 0.190 Angle : 0.661 9.543 12662 Z= 0.326 Chirality : 0.040 0.161 1484 Planarity : 0.005 0.084 1602 Dihedral : 5.188 76.935 1318 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.97 % 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: 2.41 (0.25), residues: 1164 helix: 2.52 (0.19), residues: 754 sheet: 0.45 (0.54), residues: 80 loop : -0.31 (0.34), residues: 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.100 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 90 average time/residue: 0.1829 time to fit residues: 25.3532 Evaluate side-chains 80 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0811 time to fit residues: 1.7463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.0570 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9312 Z= 0.199 Angle : 0.658 9.635 12662 Z= 0.321 Chirality : 0.039 0.172 1484 Planarity : 0.004 0.036 1602 Dihedral : 5.102 73.228 1318 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.75 % 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: 2.47 (0.25), residues: 1164 helix: 2.58 (0.19), residues: 752 sheet: 0.52 (0.54), residues: 80 loop : -0.32 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.036 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.1819 time to fit residues: 23.9354 Evaluate side-chains 81 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0958 time to fit residues: 2.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 9312 Z= 0.358 Angle : 0.741 9.629 12662 Z= 0.377 Chirality : 0.042 0.209 1484 Planarity : 0.005 0.035 1602 Dihedral : 5.483 73.246 1318 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1164 helix: 2.24 (0.19), residues: 752 sheet: 0.21 (0.55), residues: 80 loop : -0.45 (0.34), residues: 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.058 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.1684 time to fit residues: 21.6013 Evaluate side-chains 79 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0873 time to fit residues: 1.5484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 125 HIS B 293 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050836 restraints weight = 43140.166| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 5.49 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9312 Z= 0.200 Angle : 0.680 10.125 12662 Z= 0.331 Chirality : 0.040 0.182 1484 Planarity : 0.004 0.034 1602 Dihedral : 5.158 71.566 1318 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.11 % 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: 2.31 (0.25), residues: 1164 helix: 2.50 (0.19), residues: 750 sheet: 0.29 (0.56), residues: 80 loop : -0.45 (0.34), residues: 334 =============================================================================== Job complete usr+sys time: 1723.41 seconds wall clock time: 32 minutes 11.74 seconds (1931.74 seconds total)