Starting phenix.real_space_refine on Sat Mar 16 00:43:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/03_2024/7tt7_26113.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/03_2024/7tt7_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_26113/03_2024/7tt7_26113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/03_2024/7tt7_26113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/03_2024/7tt7_26113.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt7_26113/03_2024/7tt7_26113.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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 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. 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-5265/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: 6.27, per 1000 atoms: 0.47 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: 10.22 Conformation dependent library (CDL) restraints added in 1.4 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: 1.23 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: 4.84 Time building geometry restraints manager: 10.68 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: 6019 17.82 - 35.64: 200 35.64 - 53.46: 121 53.46 - 71.28: 46 71.28 - 89.10: 4 Dihedral angle restraints: 6390 sinusoidal: 3362 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 6387 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 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: 0.580 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: 0.210 Extract box with map and model: 3.440 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 44.670 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 % Allowed : 0.28 % Favored : 99.72 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P1042 HIS 0.002 0.001 HIS A 533 PHE 0.013 0.001 PHE A 652 TYR 0.019 0.002 TYR A 416 ARG 0.012 0.001 ARG A 314 *********************** 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 : 1.112 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 REVERT: A 355 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8652 (mm-30) REVERT: A 362 ASP cc_start: 0.8985 (t70) cc_final: 0.8729 (t0) REVERT: A 390 ASN cc_start: 0.9511 (m-40) cc_final: 0.9270 (m110) REVERT: A 430 ILE cc_start: 0.8925 (tt) cc_final: 0.8705 (tt) REVERT: A 441 GLN cc_start: 0.8785 (tt0) cc_final: 0.8426 (pm20) REVERT: A 515 LEU cc_start: 0.9372 (tp) cc_final: 0.9092 (pp) REVERT: A 607 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9330 (mm-30) REVERT: A 709 ASN cc_start: 0.8791 (m110) cc_final: 0.8443 (m110) REVERT: A 745 TRP cc_start: 0.8303 (p90) cc_final: 0.8093 (p90) REVERT: E 64 MET cc_start: 0.9210 (mtp) cc_final: 0.8950 (mmm) REVERT: D 115 THR cc_start: 0.7078 (m) cc_final: 0.6419 (p) REVERT: D 117 MET cc_start: 0.9113 (mmm) cc_final: 0.8697 (mmm) REVERT: D 171 LYS cc_start: 0.9402 (mmtt) cc_final: 0.8841 (mmmt) REVERT: D 176 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8783 (tppt) REVERT: D 178 GLU cc_start: 0.9023 (mm-30) cc_final: 0.7669 (mm-30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.4871 time to fit residues: 147.6111 Evaluate side-chains 164 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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: 2.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS A 579 ASN ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6976 Z= 0.222 Angle : 0.589 12.781 9434 Z= 0.334 Chirality : 0.044 0.218 993 Planarity : 0.004 0.057 1228 Dihedral : 5.181 59.516 943 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 1.01 (0.29), residues: 819 helix: 1.16 (0.45), residues: 126 sheet: 1.08 (0.26), residues: 355 loop : 0.14 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 745 HIS 0.008 0.002 HIS D 139 PHE 0.021 0.002 PHE P1296 TYR 0.013 0.001 TYR A 416 ARG 0.004 0.001 ARG A 592 *********************** 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 179 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.063 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: A 355 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8547 (mm-30) REVERT: A 390 ASN cc_start: 0.9525 (m-40) cc_final: 0.9300 (m110) REVERT: A 417 LYS cc_start: 0.9324 (tttt) cc_final: 0.8971 (ttmm) REVERT: A 550 TYR cc_start: 0.8482 (m-10) cc_final: 0.8204 (m-10) REVERT: A 579 ASN cc_start: 0.8205 (m-40) cc_final: 0.7788 (m110) REVERT: A 598 LYS cc_start: 0.9502 (ptmt) cc_final: 0.9265 (ptmt) REVERT: A 607 GLU cc_start: 0.9563 (mt-10) cc_final: 0.9338 (mm-30) REVERT: A 760 TYR cc_start: 0.7770 (m-80) cc_final: 0.7320 (m-10) REVERT: E 64 MET cc_start: 0.9239 (mtp) cc_final: 0.8817 (mmm) REVERT: E 105 ASP cc_start: 0.8077 (t70) cc_final: 0.7644 (t0) REVERT: D 115 THR cc_start: 0.7246 (m) cc_final: 0.6297 (p) REVERT: D 117 MET cc_start: 0.9147 (mmm) cc_final: 0.8697 (mmm) REVERT: D 139 HIS cc_start: 0.9375 (m90) cc_final: 0.9031 (m90) REVERT: D 171 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9065 (mmmt) REVERT: D 172 ASP cc_start: 0.8937 (m-30) cc_final: 0.8412 (p0) REVERT: D 176 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8723 (tppt) REVERT: D 178 GLU cc_start: 0.8721 (mm-30) cc_final: 0.7787 (mm-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4669 time to fit residues: 107.3726 Evaluate side-chains 144 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 82 optimal weight: 40.0000 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 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: 0.6710 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6976 Z= 0.192 Angle : 0.531 7.379 9434 Z= 0.297 Chirality : 0.043 0.167 993 Planarity : 0.004 0.033 1228 Dihedral : 5.054 61.773 943 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 819 helix: 1.02 (0.44), residues: 129 sheet: 0.69 (0.25), residues: 354 loop : -0.10 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 776 HIS 0.004 0.001 HIS D 139 PHE 0.011 0.001 PHE A 428 TYR 0.011 0.001 TYR A 416 ARG 0.003 0.000 ARG A 661 *********************** 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 167 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.085 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: A 355 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8584 (mm-30) REVERT: A 390 ASN cc_start: 0.9508 (m-40) cc_final: 0.9246 (m110) REVERT: A 447 ASP cc_start: 0.8547 (m-30) cc_final: 0.8205 (p0) REVERT: A 598 LYS cc_start: 0.9529 (ptmt) cc_final: 0.9297 (ptmt) REVERT: A 760 TYR cc_start: 0.7833 (m-80) cc_final: 0.7382 (m-10) REVERT: E 64 MET cc_start: 0.9153 (mtp) cc_final: 0.8782 (mmm) REVERT: E 105 ASP cc_start: 0.8130 (t70) cc_final: 0.7815 (t70) REVERT: D 115 THR cc_start: 0.7317 (m) cc_final: 0.6461 (p) REVERT: D 117 MET cc_start: 0.9094 (mmm) cc_final: 0.8701 (mmm) REVERT: D 139 HIS cc_start: 0.9363 (m-70) cc_final: 0.8894 (m90) REVERT: D 171 LYS cc_start: 0.9417 (mmtt) cc_final: 0.9049 (mmmt) REVERT: D 176 LYS cc_start: 0.9223 (mtmt) cc_final: 0.8738 (tppt) REVERT: D 187 GLU cc_start: 0.8933 (tt0) cc_final: 0.8712 (tt0) REVERT: P 1222 THR cc_start: 0.9045 (p) cc_final: 0.8840 (p) REVERT: P 1258 MET cc_start: 0.7655 (mmm) cc_final: 0.7026 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.4323 time to fit residues: 93.7620 Evaluate side-chains 143 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 30.0000 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 21 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6976 Z= 0.337 Angle : 0.631 7.317 9434 Z= 0.357 Chirality : 0.042 0.155 993 Planarity : 0.005 0.052 1228 Dihedral : 5.607 70.549 943 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.27), residues: 819 helix: -0.24 (0.41), residues: 128 sheet: 0.21 (0.25), residues: 346 loop : -0.82 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.010 0.001 HIS D 139 PHE 0.019 0.002 PHE E 74 TYR 0.021 0.002 TYR A 416 ARG 0.008 0.001 ARG A 367 *********************** 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 145 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.148 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: A 372 MET cc_start: 0.8190 (mmp) cc_final: 0.7460 (mmp) REVERT: A 428 PHE cc_start: 0.8516 (t80) cc_final: 0.8130 (t80) REVERT: A 447 ASP cc_start: 0.8717 (m-30) cc_final: 0.8363 (p0) REVERT: A 598 LYS cc_start: 0.9631 (ptmt) cc_final: 0.9389 (ptmt) REVERT: A 760 TYR cc_start: 0.8067 (m-80) cc_final: 0.7542 (m-10) REVERT: A 783 LEU cc_start: 0.9172 (mt) cc_final: 0.8955 (mp) REVERT: E 105 ASP cc_start: 0.8344 (t70) cc_final: 0.7985 (t70) REVERT: D 115 THR cc_start: 0.7663 (m) cc_final: 0.6787 (p) REVERT: D 117 MET cc_start: 0.9125 (mmm) cc_final: 0.8748 (mmm) REVERT: P 1258 MET cc_start: 0.7737 (mmm) cc_final: 0.7324 (tpp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.4680 time to fit residues: 87.8542 Evaluate side-chains 128 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 579 ASN A 606 ASN A 709 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6976 Z= 0.249 Angle : 0.564 6.110 9434 Z= 0.314 Chirality : 0.042 0.144 993 Planarity : 0.004 0.043 1228 Dihedral : 5.647 81.246 943 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.14 % Allowed : 1.40 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.27), residues: 819 helix: -0.31 (0.42), residues: 128 sheet: 0.11 (0.25), residues: 345 loop : -0.87 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 191 HIS 0.005 0.001 HIS D 139 PHE 0.012 0.002 PHE A 440 TYR 0.019 0.001 TYR A 416 ARG 0.004 0.001 ARG A 366 *********************** 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 146 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.018 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: A 428 PHE cc_start: 0.8476 (t80) cc_final: 0.8259 (t80) REVERT: A 492 ASN cc_start: 0.9366 (t0) cc_final: 0.8940 (t0) REVERT: A 598 LYS cc_start: 0.9638 (ptmt) cc_final: 0.9397 (ptmt) REVERT: A 606 ASN cc_start: 0.8848 (m-40) cc_final: 0.8387 (m110) REVERT: A 768 MET cc_start: 0.8029 (ptp) cc_final: 0.7561 (ptt) REVERT: E 50 MET cc_start: 0.8682 (ttm) cc_final: 0.8230 (ttm) REVERT: E 105 ASP cc_start: 0.8388 (t70) cc_final: 0.8033 (t70) REVERT: E 110 LEU cc_start: 0.8998 (tt) cc_final: 0.8268 (mp) REVERT: D 115 THR cc_start: 0.7741 (m) cc_final: 0.6909 (p) REVERT: D 117 MET cc_start: 0.9106 (mmm) cc_final: 0.8748 (mmm) REVERT: D 139 HIS cc_start: 0.9259 (m-70) cc_final: 0.8615 (m-70) REVERT: D 177 TYR cc_start: 0.9469 (t80) cc_final: 0.9258 (t80) outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.4442 time to fit residues: 84.2950 Evaluate side-chains 128 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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: 0.7980 chunk 73 optimal weight: 30.0000 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6976 Z= 0.137 Angle : 0.478 4.613 9434 Z= 0.263 Chirality : 0.042 0.155 993 Planarity : 0.004 0.035 1228 Dihedral : 5.313 86.227 943 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -0.24 (0.28), residues: 819 helix: 0.42 (0.44), residues: 130 sheet: 0.18 (0.26), residues: 340 loop : -0.61 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 280 PHE 0.009 0.001 PHE A 428 TYR 0.011 0.001 TYR A 416 ARG 0.001 0.000 ARG P1205 *********************** 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 152 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.070 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: A 361 LYS cc_start: 0.8273 (tttt) cc_final: 0.7955 (mtpt) REVERT: A 369 MET cc_start: 0.9246 (mmp) cc_final: 0.9028 (mmt) REVERT: A 428 PHE cc_start: 0.8424 (t80) cc_final: 0.8209 (t80) REVERT: A 470 GLU cc_start: 0.7641 (mp0) cc_final: 0.7390 (mp0) REVERT: A 511 THR cc_start: 0.9124 (t) cc_final: 0.8875 (t) REVERT: A 521 GLU cc_start: 0.9235 (pt0) cc_final: 0.9016 (pt0) REVERT: A 598 LYS cc_start: 0.9627 (ptmt) cc_final: 0.9404 (ptmt) REVERT: A 606 ASN cc_start: 0.8997 (m-40) cc_final: 0.8522 (m110) REVERT: A 760 TYR cc_start: 0.7971 (m-80) cc_final: 0.7542 (m-10) REVERT: A 768 MET cc_start: 0.7978 (ptp) cc_final: 0.7527 (ptt) REVERT: E 50 MET cc_start: 0.8519 (ttm) cc_final: 0.8037 (ttm) REVERT: E 105 ASP cc_start: 0.8339 (t70) cc_final: 0.8043 (t0) REVERT: D 115 THR cc_start: 0.7707 (m) cc_final: 0.6893 (p) REVERT: D 117 MET cc_start: 0.9114 (mmm) cc_final: 0.8777 (mmm) REVERT: D 139 HIS cc_start: 0.9194 (m-70) cc_final: 0.8621 (m-70) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4216 time to fit residues: 83.4834 Evaluate side-chains 131 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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: 0.4980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.5600 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= 0.177 Angle : 0.494 5.120 9434 Z= 0.273 Chirality : 0.042 0.150 993 Planarity : 0.004 0.034 1228 Dihedral : 5.240 83.215 943 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.20 (0.28), residues: 819 helix: 0.51 (0.45), residues: 129 sheet: 0.16 (0.26), residues: 341 loop : -0.56 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 191 HIS 0.004 0.001 HIS D 139 PHE 0.009 0.001 PHE A 428 TYR 0.010 0.001 TYR D 177 ARG 0.004 0.000 ARG A 391 *********************** 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 145 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.099 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: A 308 ILE cc_start: 0.9492 (mt) cc_final: 0.9161 (tp) REVERT: A 521 GLU cc_start: 0.9148 (pt0) cc_final: 0.8846 (pt0) REVERT: A 606 ASN cc_start: 0.9014 (m-40) cc_final: 0.8164 (m110) REVERT: A 608 TYR cc_start: 0.9107 (p90) cc_final: 0.8690 (p90) REVERT: A 760 TYR cc_start: 0.8014 (m-80) cc_final: 0.7575 (m-10) REVERT: A 768 MET cc_start: 0.8000 (ptp) cc_final: 0.7568 (ptt) REVERT: C 50 LEU cc_start: 0.8392 (mp) cc_final: 0.8165 (mp) REVERT: E 50 MET cc_start: 0.8598 (ttm) cc_final: 0.8180 (ttm) REVERT: E 105 ASP cc_start: 0.8355 (t70) cc_final: 0.8056 (t70) REVERT: D 115 THR cc_start: 0.7686 (m) cc_final: 0.6903 (p) REVERT: D 117 MET cc_start: 0.9115 (mmm) cc_final: 0.8772 (mmm) REVERT: P 1267 GLU cc_start: 0.8528 (mp0) cc_final: 0.8300 (mp0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.4468 time to fit residues: 83.7779 Evaluate side-chains 128 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 0.0040 chunk 40 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 overall best weight: 0.9514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.5711 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= 0.133 Angle : 0.470 4.601 9434 Z= 0.256 Chirality : 0.042 0.155 993 Planarity : 0.004 0.035 1228 Dihedral : 5.059 81.055 943 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.03 (0.29), residues: 819 helix: 0.72 (0.45), residues: 130 sheet: 0.31 (0.26), residues: 334 loop : -0.41 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 191 HIS 0.004 0.001 HIS D 139 PHE 0.014 0.001 PHE A 428 TYR 0.010 0.001 TYR D 177 ARG 0.002 0.000 ARG A 391 *********************** 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 148 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.083 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: A 308 ILE cc_start: 0.9506 (mt) cc_final: 0.9158 (tp) REVERT: A 369 MET cc_start: 0.9105 (mmt) cc_final: 0.8631 (mmt) REVERT: A 521 GLU cc_start: 0.9148 (pt0) cc_final: 0.8832 (pt0) REVERT: A 598 LYS cc_start: 0.9605 (ptmt) cc_final: 0.9397 (ptmt) REVERT: A 606 ASN cc_start: 0.9008 (m-40) cc_final: 0.8177 (m110) REVERT: A 608 TYR cc_start: 0.9072 (p90) cc_final: 0.8619 (p90) REVERT: A 760 TYR cc_start: 0.7999 (m-80) cc_final: 0.7584 (m-10) REVERT: A 768 MET cc_start: 0.7963 (ptp) cc_final: 0.7523 (ptt) REVERT: E 50 MET cc_start: 0.8513 (ttm) cc_final: 0.8061 (ttm) REVERT: E 105 ASP cc_start: 0.8435 (t70) cc_final: 0.8156 (t0) REVERT: D 115 THR cc_start: 0.7711 (m) cc_final: 0.7068 (p) REVERT: D 117 MET cc_start: 0.9122 (mmm) cc_final: 0.8525 (mmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.4201 time to fit residues: 81.0783 Evaluate side-chains 134 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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: 40.0000 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN A 709 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6976 Z= 0.352 Angle : 0.625 7.775 9434 Z= 0.350 Chirality : 0.043 0.149 993 Planarity : 0.005 0.054 1228 Dihedral : 5.588 77.546 943 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.77 (0.28), residues: 819 helix: -0.44 (0.42), residues: 129 sheet: -0.04 (0.26), residues: 346 loop : -0.89 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 576 HIS 0.003 0.001 HIS D 139 PHE 0.019 0.002 PHE D 144 TYR 0.012 0.002 TYR A 348 ARG 0.006 0.001 ARG A 366 *********************** 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 133 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.076 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: A 305 GLU cc_start: 0.9113 (tt0) cc_final: 0.8765 (mt-10) REVERT: A 511 THR cc_start: 0.9015 (t) cc_final: 0.8782 (t) REVERT: A 521 GLU cc_start: 0.8989 (pt0) cc_final: 0.8776 (pt0) REVERT: A 598 LYS cc_start: 0.9611 (ptmt) cc_final: 0.9306 (ptmt) REVERT: A 606 ASN cc_start: 0.9098 (m-40) cc_final: 0.8617 (m110) REVERT: A 711 MET cc_start: 0.9046 (ppp) cc_final: 0.8819 (ppp) REVERT: A 760 TYR cc_start: 0.8190 (m-80) cc_final: 0.7709 (m-10) REVERT: A 768 MET cc_start: 0.8053 (ptp) cc_final: 0.7595 (ptt) REVERT: E 50 MET cc_start: 0.8604 (ttm) cc_final: 0.8173 (ttm) REVERT: E 105 ASP cc_start: 0.8456 (t70) cc_final: 0.8181 (t70) REVERT: D 117 MET cc_start: 0.9074 (mmm) cc_final: 0.8709 (tmm) REVERT: P 1258 MET cc_start: 0.7777 (mmm) cc_final: 0.7423 (tpp) REVERT: P 1276 LEU cc_start: 0.8922 (mp) cc_final: 0.8575 (tp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4304 time to fit residues: 74.6469 Evaluate side-chains 119 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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: 9.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN D 139 HIS P1271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6976 Z= 0.217 Angle : 0.532 7.612 9434 Z= 0.292 Chirality : 0.042 0.153 993 Planarity : 0.004 0.044 1228 Dihedral : 5.341 74.136 943 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.63 (0.28), residues: 819 helix: -0.21 (0.42), residues: 135 sheet: 0.02 (0.27), residues: 341 loop : -0.83 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.005 0.001 HIS D 139 PHE 0.010 0.001 PHE D 144 TYR 0.013 0.001 TYR A 416 ARG 0.004 0.001 ARG A 391 ********************** 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 138 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.168 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: A 304 MET cc_start: 0.8361 (tpp) cc_final: 0.8008 (mmt) REVERT: A 305 GLU cc_start: 0.9062 (tt0) cc_final: 0.8740 (mt-10) REVERT: A 308 ILE cc_start: 0.9554 (mt) cc_final: 0.9242 (tp) REVERT: A 369 MET cc_start: 0.9060 (mmt) cc_final: 0.8852 (mmt) REVERT: A 606 ASN cc_start: 0.9115 (m-40) cc_final: 0.8241 (m110) REVERT: A 608 TYR cc_start: 0.9144 (p90) cc_final: 0.8732 (p90) REVERT: A 614 ASP cc_start: 0.8697 (t0) cc_final: 0.8446 (t0) REVERT: A 711 MET cc_start: 0.9037 (ppp) cc_final: 0.8738 (ppp) REVERT: A 768 MET cc_start: 0.8003 (ptp) cc_final: 0.7570 (ptt) REVERT: E 50 MET cc_start: 0.8522 (ttm) cc_final: 0.8063 (ttm) REVERT: E 105 ASP cc_start: 0.8455 (t70) cc_final: 0.8131 (t70) REVERT: D 117 MET cc_start: 0.9104 (mmm) cc_final: 0.8734 (tmm) REVERT: P 1258 MET cc_start: 0.7801 (mmm) cc_final: 0.7437 (tpp) REVERT: P 1267 GLU cc_start: 0.8614 (mp0) cc_final: 0.8407 (mp0) REVERT: P 1276 LEU cc_start: 0.9025 (mp) cc_final: 0.8623 (tp) REVERT: P 1295 ASN cc_start: 0.8489 (p0) cc_final: 0.8243 (p0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4659 time to fit residues: 82.8629 Evaluate side-chains 124 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN A 748 ASN D 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.112714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.080485 restraints weight = 69968.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082027 restraints weight = 32078.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083581 restraints weight = 20948.667| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6976 Z= 0.176 Angle : 0.499 6.794 9434 Z= 0.273 Chirality : 0.042 0.157 993 Planarity : 0.004 0.040 1228 Dihedral : 4.963 62.718 943 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.46 (0.29), residues: 819 helix: 0.12 (0.43), residues: 135 sheet: 0.10 (0.27), residues: 337 loop : -0.78 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 749 HIS 0.005 0.001 HIS D 139 PHE 0.008 0.001 PHE D 144 TYR 0.012 0.001 TYR D 177 ARG 0.004 0.000 ARG A 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3404.52 seconds wall clock time: 60 minutes 34.29 seconds (3634.29 seconds total)