Starting phenix.real_space_refine (version: dev) on Mon Feb 20 22:36:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/02_2023/7tt7_26113.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/02_2023/7tt7_26113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/02_2023/7tt7_26113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/02_2023/7tt7_26113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/02_2023/7tt7_26113.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/02_2023/7tt7_26113.pdb" } resolution = 4.8 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= 0.006 sd= 0.048 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 TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13296 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7625 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 477} Chain breaks: 7 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 396 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 4, 'TRANS': 23} Chain breaks: 1 Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1599 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Chain: "P" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2295 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 150} Chain breaks: 8 Time building chain proxies: 6.43, per 1000 atoms: 0.48 Number of scatterers: 13296 At special positions: 0 Unit cell: (92.3485, 94.4962, 128.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 1321 8.00 N 1158 7.00 C 4323 6.00 H 6468 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 21.0% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.076A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 366' Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.586A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.664A pdb=" N MET A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.991A pdb=" N LEU D 119 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP D 121 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 137 through 145 removed outlier: 4.070A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 189 removed outlier: 4.277A pdb=" N LEU D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 235 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 272 through 276 removed outlier: 6.528A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 355 removed outlier: 5.963A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.698A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.395A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.429A pdb=" N LEU A 783 " --> pdb=" O TRP A 776 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP A 776 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE A 785 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 428 " --> pdb=" O PHE P1296 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE P1296 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA P1294 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY P1156 " --> pdb=" O ASP P1120 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP P1120 " --> pdb=" O GLY P1156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.293A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.667A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.638A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 10.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6468 1.03 - 1.23: 15 1.23 - 1.42: 3090 1.42 - 1.62: 3823 1.62 - 1.81: 48 Bond restraints: 13444 Sorted by residual: bond pdb=" C PHE A 737 " pdb=" O PHE A 737 " ideal model delta sigma weight residual 1.234 1.221 0.013 1.22e-02 6.72e+03 1.14e+00 bond pdb=" N GLY A 631 " pdb=" CA GLY A 631 " ideal model delta sigma weight residual 1.449 1.439 0.010 1.18e-02 7.18e+03 7.41e-01 bond pdb=" CA PRO D 206 " pdb=" C PRO D 206 " ideal model delta sigma weight residual 1.516 1.531 -0.014 1.75e-02 3.27e+03 6.86e-01 bond pdb=" C TRP A 576 " pdb=" N THR A 577 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.55e-02 4.16e+03 6.75e-01 bond pdb=" N GLN A 371 " pdb=" CA GLN A 371 " ideal model delta sigma weight residual 1.458 1.447 0.010 1.24e-02 6.50e+03 6.64e-01 ... (remaining 13439 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.26: 185 106.26 - 113.21: 14998 113.21 - 120.16: 4484 120.16 - 127.11: 4311 127.11 - 134.06: 79 Bond angle restraints: 24057 Sorted by residual: angle pdb=" N GLY A 756 " pdb=" CA GLY A 756 " pdb=" C GLY A 756 " ideal model delta sigma weight residual 115.34 108.94 6.40 1.67e+00 3.59e-01 1.47e+01 angle pdb=" N PHE A 478 " pdb=" CA PHE A 478 " pdb=" C PHE A 478 " ideal model delta sigma weight residual 111.36 107.35 4.01 1.09e+00 8.42e-01 1.36e+01 angle pdb=" N ARG D 212 " pdb=" CA ARG D 212 " pdb=" C ARG D 212 " ideal model delta sigma weight residual 112.45 107.80 4.65 1.39e+00 5.18e-01 1.12e+01 angle pdb=" N ASN A 579 " pdb=" CA ASN A 579 " pdb=" C ASN A 579 " ideal model delta sigma weight residual 107.67 114.65 -6.98 2.09e+00 2.29e-01 1.12e+01 angle pdb=" N THR A 577 " pdb=" CA THR A 577 " pdb=" C THR A 577 " ideal model delta sigma weight residual 109.24 114.52 -5.28 1.67e+00 3.59e-01 9.99e+00 ... (remaining 24052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5241 17.82 - 35.64: 140 35.64 - 53.46: 43 53.46 - 71.28: 16 71.28 - 89.10: 4 Dihedral angle restraints: 5444 sinusoidal: 2416 harmonic: 3028 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 131.29 -38.29 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA VAL A 660 " pdb=" C VAL A 660 " pdb=" N ARG A 661 " pdb=" CA ARG A 661 " ideal model delta harmonic sigma weight residual -180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE A 395 " pdb=" C PHE A 395 " pdb=" N GLU A 396 " pdb=" CA GLU A 396 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 591 0.034 - 0.068: 245 0.068 - 0.102: 99 0.102 - 0.136: 46 0.136 - 0.170: 12 Chirality restraints: 993 Sorted by residual: chirality pdb=" CA ILE P1167 " pdb=" N ILE P1167 " pdb=" C ILE P1167 " pdb=" CB ILE P1167 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA TRP D 191 " pdb=" N TRP D 191 " pdb=" C TRP D 191 " pdb=" CB TRP D 191 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 990 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 544 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ALA A 544 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 544 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A 545 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 652 " 0.008 2.00e-02 2.50e+03 1.48e-02 6.58e+00 pdb=" CG PHE A 652 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 652 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 652 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 652 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 652 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 652 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 652 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE A 652 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE A 652 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 652 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 652 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 653 " -0.010 2.00e-02 2.50e+03 1.33e-02 5.34e+00 pdb=" CG TYR A 653 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 653 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 653 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 653 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 653 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 653 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 653 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 653 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 653 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR A 653 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 653 " -0.016 2.00e-02 2.50e+03 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 299 2.09 - 2.72: 22357 2.72 - 3.34: 35860 3.34 - 3.97: 46510 3.97 - 4.60: 71622 Nonbonded interactions: 176648 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 310 " pdb=" OD1 ASP A 380 " model vdw 1.460 1.850 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.479 1.850 nonbonded pdb=" H GLU A 396 " pdb=" O LYS A 419 " model vdw 1.481 1.850 nonbonded pdb=" O ASP P1270 " pdb="HH12 ARG P1273 " model vdw 1.484 1.850 nonbonded pdb="HD22 ASN E 71 " pdb=" O ASN E 96 " model vdw 1.535 1.850 ... (remaining 176643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 4323 2.51 5 N 1158 2.21 5 O 1321 1.98 5 H 6468 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.200 Extract box with map and model: 3.940 Check model and map are aligned: 0.190 Process input model: 43.600 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 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 : 0.003 0.024 6976 Z= 0.188 Angle : 0.839 6.984 9434 Z= 0.514 Chirality : 0.048 0.170 993 Planarity : 0.005 0.027 1228 Dihedral : 10.502 89.098 2476 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 0.00 % 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: 0.94 (0.28), residues: 819 helix: -0.22 (0.41), residues: 116 sheet: 1.37 (0.26), residues: 357 loop : 0.22 (0.33), residues: 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.4939 time to fit residues: 150.0334 Evaluate side-chains 159 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.0570 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 HIS A 579 ASN A 709 ASN D 139 HIS ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 6976 Z= 0.175 Angle : 0.577 14.328 9434 Z= 0.324 Chirality : 0.045 0.247 993 Planarity : 0.004 0.043 1228 Dihedral : 5.004 58.554 943 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.00 % 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: 1.24 (0.29), residues: 819 helix: 1.40 (0.46), residues: 122 sheet: 1.22 (0.26), residues: 352 loop : 0.29 (0.34), residues: 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.4468 time to fit residues: 107.1287 Evaluate side-chains 143 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN D 139 HIS ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 6976 Z= 0.179 Angle : 0.531 8.977 9434 Z= 0.297 Chirality : 0.043 0.190 993 Planarity : 0.003 0.027 1228 Dihedral : 4.910 58.462 943 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.00 % 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: 0.84 (0.28), residues: 819 helix: 1.15 (0.44), residues: 128 sheet: 0.82 (0.26), residues: 354 loop : 0.17 (0.34), residues: 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.4398 time to fit residues: 95.1927 Evaluate side-chains 142 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 72 optimal weight: 50.0000 chunk 21 optimal weight: 0.2980 overall best weight: 1.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN D 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6976 Z= 0.213 Angle : 0.537 5.317 9434 Z= 0.299 Chirality : 0.042 0.171 993 Planarity : 0.004 0.029 1228 Dihedral : 5.389 84.542 943 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.14 % 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: 0.32 (0.28), residues: 819 helix: 0.70 (0.44), residues: 130 sheet: 0.53 (0.25), residues: 352 loop : -0.20 (0.33), residues: 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.4218 time to fit residues: 86.6650 Evaluate side-chains 137 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1350 time to fit residues: 1.5477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 69 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN E 34 GLN D 139 HIS D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6976 Z= 0.181 Angle : 0.512 4.894 9434 Z= 0.282 Chirality : 0.042 0.147 993 Planarity : 0.003 0.029 1228 Dihedral : 5.195 79.303 943 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.00 % 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: 0.18 (0.28), residues: 819 helix: 0.70 (0.45), residues: 130 sheet: 0.34 (0.25), residues: 355 loop : -0.21 (0.34), residues: 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.4373 time to fit residues: 86.8071 Evaluate side-chains 134 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 606 ASN A 709 ASN D 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 6976 Z= 0.149 Angle : 0.480 4.820 9434 Z= 0.263 Chirality : 0.042 0.144 993 Planarity : 0.003 0.030 1228 Dihedral : 4.989 72.571 943 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % 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: 0.18 (0.28), residues: 819 helix: 0.81 (0.45), residues: 130 sheet: 0.34 (0.25), residues: 345 loop : -0.24 (0.34), residues: 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.4218 time to fit residues: 84.9238 Evaluate side-chains 133 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 606 ASN A 709 ASN D 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 6976 Z= 0.238 Angle : 0.538 5.348 9434 Z= 0.300 Chirality : 0.042 0.142 993 Planarity : 0.004 0.029 1228 Dihedral : 5.049 66.525 943 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.00 % 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: -0.09 (0.28), residues: 819 helix: 0.49 (0.45), residues: 129 sheet: 0.29 (0.26), residues: 346 loop : -0.53 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4550 time to fit residues: 86.6267 Evaluate side-chains 132 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN A 606 ASN A 709 ASN D 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6976 Z= 0.212 Angle : 0.525 6.023 9434 Z= 0.288 Chirality : 0.042 0.141 993 Planarity : 0.004 0.036 1228 Dihedral : 4.953 58.329 943 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.00 % 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: -0.18 (0.28), residues: 819 helix: 0.29 (0.44), residues: 128 sheet: 0.23 (0.26), residues: 355 loop : -0.52 (0.34), residues: 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.4615 time to fit residues: 87.1172 Evaluate side-chains 126 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 606 ASN A 709 ASN D 139 HIS P1271 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6976 Z= 0.239 Angle : 0.550 6.108 9434 Z= 0.303 Chirality : 0.042 0.143 993 Planarity : 0.004 0.042 1228 Dihedral : 4.927 50.550 943 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.00 % 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: -0.45 (0.28), residues: 819 helix: -0.07 (0.43), residues: 128 sheet: 0.11 (0.26), residues: 348 loop : -0.68 (0.33), residues: 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.4461 time to fit residues: 81.0286 Evaluate side-chains 125 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.0040 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 606 ASN A 709 ASN D 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6976 Z= 0.181 Angle : 0.516 6.463 9434 Z= 0.281 Chirality : 0.042 0.148 993 Planarity : 0.004 0.036 1228 Dihedral : 4.748 43.111 943 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.00 % 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: -0.30 (0.28), residues: 819 helix: 0.08 (0.43), residues: 128 sheet: 0.20 (0.27), residues: 340 loop : -0.59 (0.33), residues: 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.4338 time to fit residues: 82.1933 Evaluate side-chains 129 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 606 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.114469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.081504 restraints weight = 70034.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083723 restraints weight = 30900.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085160 restraints weight = 19671.777| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 6976 Z= 0.144 Angle : 0.492 6.382 9434 Z= 0.267 Chirality : 0.042 0.143 993 Planarity : 0.003 0.032 1228 Dihedral : 4.517 33.755 943 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.00 % 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: -0.18 (0.29), residues: 819 helix: 0.21 (0.44), residues: 136 sheet: 0.27 (0.26), residues: 346 loop : -0.53 (0.34), residues: 337 =============================================================================== Job complete usr+sys time: 3350.11 seconds wall clock time: 59 minutes 37.56 seconds (3577.56 seconds total)