Starting phenix.real_space_refine on Tue Sep 24 00:20:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyq_60576/09_2024/8zyq_60576.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyq_60576/09_2024/8zyq_60576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyq_60576/09_2024/8zyq_60576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyq_60576/09_2024/8zyq_60576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyq_60576/09_2024/8zyq_60576.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyq_60576/09_2024/8zyq_60576.cif" } resolution = 3.18 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= 0.001 sd= 0.023 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 31 5.16 5 C 4252 2.51 5 N 1019 2.21 5 O 1025 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6329 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1309 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1662 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1662 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1662 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'1II': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.04, per 1000 atoms: 0.80 Number of scatterers: 6329 At special positions: 0 Unit cell: (107.9, 110.39, 76.36, 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 31 16.00 F 2 9.00 O 1025 8.00 N 1019 7.00 C 4252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.60 Conformation dependent library (CDL) restraints added in 865.8 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 409 through 432 removed outlier: 3.563A pdb=" N LEU A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.572A pdb=" N LEU A 524 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 576 Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.519A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 663 Processing helix chain 'B' and resid 409 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 453 through 471 removed outlier: 4.066A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 497 removed outlier: 3.505A pdb=" N LYS B 495 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 Processing helix chain 'B' and resid 520 through 530 Processing helix chain 'B' and resid 531 through 538 removed outlier: 4.178A pdb=" N VAL B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.768A pdb=" N TYR B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 575 Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.531A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 665 removed outlier: 3.727A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 431 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 453 through 470 Processing helix chain 'C' and resid 489 through 496 Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 520 through 530 removed outlier: 3.898A pdb=" N LEU C 524 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS C 525 " --> pdb=" O GLY C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 538 removed outlier: 3.969A pdb=" N VAL C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.647A pdb=" N TYR C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 575 removed outlier: 3.517A pdb=" N GLU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.619A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 665 removed outlier: 3.701A pdb=" N GLN C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 432 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 453 through 471 removed outlier: 3.920A pdb=" N PHE D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 495 Processing helix chain 'D' and resid 497 through 506 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.994A pdb=" N LEU D 530 " --> pdb=" O ALA D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 547 through 574 removed outlier: 3.510A pdb=" N MET D 574 " --> pdb=" O ALA D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 663 460 hydrogen bonds defined for protein. 1308 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: 1.65 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 908 1.31 - 1.44: 1894 1.44 - 1.56: 3633 1.56 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 6485 Sorted by residual: bond pdb=" C34 1II B1101 " pdb=" F02 1II B1101 " ideal model delta sigma weight residual 1.344 1.189 0.155 2.00e-02 2.50e+03 5.98e+01 bond pdb=" C17 1II B1101 " pdb=" C20 1II B1101 " ideal model delta sigma weight residual 1.517 1.396 0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C17 1II B1101 " pdb=" C21 1II B1101 " ideal model delta sigma weight residual 1.514 1.402 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C14 1II B1101 " pdb=" C18 1II B1101 " ideal model delta sigma weight residual 1.400 1.334 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C14 1II B1101 " pdb=" C19 1II B1101 " ideal model delta sigma weight residual 1.383 1.322 0.061 2.00e-02 2.50e+03 9.38e+00 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8673 2.13 - 4.26: 100 4.26 - 6.39: 21 6.39 - 8.53: 3 8.53 - 10.66: 1 Bond angle restraints: 8798 Sorted by residual: angle pdb=" C11 1II B1101 " pdb=" N04 1II B1101 " pdb=" C12 1II B1101 " ideal model delta sigma weight residual 116.12 105.46 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C07 1II B1101 " pdb=" N05 1II B1101 " pdb=" C14 1II B1101 " ideal model delta sigma weight residual 125.68 133.71 -8.03 3.00e+00 1.11e-01 7.16e+00 angle pdb=" C13 1II B1101 " pdb=" C15 1II B1101 " pdb=" C17 1II B1101 " ideal model delta sigma weight residual 114.42 106.47 7.95 3.00e+00 1.11e-01 7.03e+00 angle pdb=" C PHE D 424 " pdb=" N THR D 425 " pdb=" CA THR D 425 " ideal model delta sigma weight residual 121.80 115.49 6.31 2.44e+00 1.68e-01 6.68e+00 angle pdb=" C ILE D 655 " pdb=" N PHE D 656 " pdb=" CA PHE D 656 " ideal model delta sigma weight residual 122.06 117.43 4.63 1.86e+00 2.89e-01 6.18e+00 ... (remaining 8793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 3535 29.97 - 59.94: 171 59.94 - 89.91: 8 89.91 - 119.88: 2 119.88 - 149.85: 2 Dihedral angle restraints: 3718 sinusoidal: 1421 harmonic: 2297 Sorted by residual: dihedral pdb=" C10 1II B1101 " pdb=" C12 1II B1101 " pdb=" N04 1II B1101 " pdb=" C13 1II B1101 " ideal model delta sinusoidal sigma weight residual 77.41 -72.44 149.85 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C11 1II B1101 " pdb=" C12 1II B1101 " pdb=" N04 1II B1101 " pdb=" C13 1II B1101 " ideal model delta sinusoidal sigma weight residual 301.46 168.34 133.12 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA PHE D 656 " pdb=" C PHE D 656 " pdb=" N GLY D 657 " pdb=" CA GLY D 657 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 3715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 726 0.036 - 0.073: 241 0.073 - 0.109: 55 0.109 - 0.146: 7 0.146 - 0.182: 3 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C07 1II B1101 " pdb=" C08 1II B1101 " pdb=" C09 1II B1101 " pdb=" N05 1II B1101 " both_signs ideal model delta sigma weight residual False -2.31 -2.49 0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA THR D 425 " pdb=" N THR D 425 " pdb=" C THR D 425 " pdb=" CB THR D 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA PHE D 656 " pdb=" N PHE D 656 " pdb=" C PHE D 656 " pdb=" CB PHE D 656 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1029 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 576 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO D 577 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 656 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C PHE D 656 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE D 656 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY D 657 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 656 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C PHE C 656 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE C 656 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 657 " 0.008 2.00e-02 2.50e+03 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1232 2.77 - 3.30: 6115 3.30 - 3.83: 10712 3.83 - 4.37: 11532 4.37 - 4.90: 20532 Nonbonded interactions: 50123 Sorted by model distance: nonbonded pdb=" O PHE B 619 " pdb=" OG1 THR B 623 " model vdw 2.234 3.040 nonbonded pdb=" O SER D 543 " pdb=" OG SER D 543 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR B 493 " pdb=" OD2 ASP B 501 " model vdw 2.259 3.040 nonbonded pdb=" N GLN A 664 " pdb=" OE1 GLN A 664 " model vdw 2.284 3.120 nonbonded pdb=" O THR A 421 " pdb=" OG1 THR A 425 " model vdw 2.285 3.040 ... (remaining 50118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 407 through 665) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.630 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.005 0.155 6485 Z= 0.281 Angle : 0.586 10.656 8798 Z= 0.287 Chirality : 0.038 0.182 1032 Planarity : 0.004 0.048 1033 Dihedral : 16.950 149.851 2234 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.46 % Allowed : 24.73 % Favored : 74.81 % 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: 1.48 (0.31), residues: 752 helix: 1.20 (0.21), residues: 635 sheet: None (None), residues: 0 loop : 0.17 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 568 HIS 0.003 0.001 HIS D 562 PHE 0.018 0.001 PHE D 656 TYR 0.018 0.002 TYR B 616 ARG 0.008 0.001 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.664 Fit side-chains REVERT: A 576 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8082 (tm-30) REVERT: B 494 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7427 (m-10) REVERT: B 633 ASN cc_start: 0.8937 (t0) cc_final: 0.8570 (t0) REVERT: C 528 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.7950 (ttt90) REVERT: C 652 TYR cc_start: 0.5799 (t80) cc_final: 0.4415 (t80) outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.2045 time to fit residues: 26.3748 Evaluate side-chains 98 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 494 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 664 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6485 Z= 0.189 Angle : 0.522 6.885 8798 Z= 0.275 Chirality : 0.039 0.155 1032 Planarity : 0.004 0.041 1033 Dihedral : 9.334 128.157 876 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.43 % Allowed : 24.13 % Favored : 73.44 % 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: 1.53 (0.31), residues: 752 helix: 1.22 (0.21), residues: 641 sheet: None (None), residues: 0 loop : 0.22 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 568 HIS 0.003 0.001 HIS D 562 PHE 0.015 0.001 PHE C 656 TYR 0.018 0.002 TYR B 616 ARG 0.003 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.663 Fit side-chains REVERT: A 576 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 597 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: B 488 ARG cc_start: 0.2174 (OUTLIER) cc_final: 0.1771 (ppt170) REVERT: B 633 ASN cc_start: 0.9000 (t0) cc_final: 0.8613 (t0) REVERT: C 528 ARG cc_start: 0.8539 (mtp-110) cc_final: 0.8018 (ttt90) REVERT: D 629 ASN cc_start: 0.7668 (t0) cc_final: 0.7456 (t0) outliers start: 16 outliers final: 9 residues processed: 115 average time/residue: 0.1933 time to fit residues: 28.8951 Evaluate side-chains 110 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 574 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN D 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6485 Z= 0.201 Angle : 0.511 6.920 8798 Z= 0.269 Chirality : 0.039 0.179 1032 Planarity : 0.003 0.036 1033 Dihedral : 7.767 75.981 874 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.95 % Allowed : 24.73 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.31), residues: 752 helix: 1.26 (0.21), residues: 641 sheet: None (None), residues: 0 loop : 0.15 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.003 0.001 HIS D 562 PHE 0.018 0.001 PHE C 656 TYR 0.018 0.002 TYR B 616 ARG 0.006 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.583 Fit side-chains REVERT: A 576 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 597 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: B 488 ARG cc_start: 0.2531 (OUTLIER) cc_final: 0.1843 (ppt170) REVERT: B 520 LEU cc_start: 0.6550 (tp) cc_final: 0.6325 (tt) REVERT: B 633 ASN cc_start: 0.8982 (t0) cc_final: 0.8603 (t0) REVERT: C 528 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8096 (ttt90) REVERT: C 651 MET cc_start: 0.8670 (tpp) cc_final: 0.8354 (tpp) REVERT: C 655 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7032 (mt) outliers start: 26 outliers final: 12 residues processed: 121 average time/residue: 0.1904 time to fit residues: 30.0138 Evaluate side-chains 114 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 647 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.0030 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN D 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6485 Z= 0.166 Angle : 0.491 6.819 8798 Z= 0.256 Chirality : 0.038 0.189 1032 Planarity : 0.003 0.034 1033 Dihedral : 7.363 73.619 874 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.79 % Allowed : 25.34 % Favored : 70.86 % 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: 1.75 (0.32), residues: 752 helix: 1.40 (0.21), residues: 638 sheet: None (None), residues: 0 loop : 0.16 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.002 0.001 HIS D 562 PHE 0.013 0.001 PHE C 656 TYR 0.016 0.002 TYR B 616 ARG 0.006 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.447 Fit side-chains REVERT: A 576 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 597 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: B 488 ARG cc_start: 0.2398 (OUTLIER) cc_final: 0.1765 (ppt170) REVERT: B 633 ASN cc_start: 0.8966 (t0) cc_final: 0.8579 (t0) REVERT: C 528 ARG cc_start: 0.8568 (mtp-110) cc_final: 0.8092 (ttt90) REVERT: C 552 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7525 (mm) REVERT: C 651 MET cc_start: 0.8639 (tpp) cc_final: 0.8412 (tpp) REVERT: C 652 TYR cc_start: 0.5977 (t80) cc_final: 0.5106 (t80) outliers start: 25 outliers final: 12 residues processed: 121 average time/residue: 0.1368 time to fit residues: 21.4423 Evaluate side-chains 113 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 545 TYR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN A 578 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6485 Z= 0.152 Angle : 0.482 6.820 8798 Z= 0.249 Chirality : 0.038 0.173 1032 Planarity : 0.003 0.031 1033 Dihedral : 7.301 74.618 874 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.95 % Allowed : 25.19 % Favored : 70.86 % 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: 1.82 (0.32), residues: 752 helix: 1.45 (0.21), residues: 641 sheet: None (None), residues: 0 loop : 0.15 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.002 0.001 HIS D 562 PHE 0.013 0.001 PHE C 656 TYR 0.015 0.001 TYR B 616 ARG 0.006 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 0.503 Fit side-chains REVERT: A 576 GLN cc_start: 0.8268 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 597 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 488 ARG cc_start: 0.2310 (OUTLIER) cc_final: 0.1675 (ppt170) REVERT: B 499 LEU cc_start: 0.7318 (pt) cc_final: 0.6986 (pp) REVERT: B 573 ASN cc_start: 0.8896 (t0) cc_final: 0.8543 (t0) REVERT: B 633 ASN cc_start: 0.8958 (t0) cc_final: 0.8548 (t0) REVERT: C 528 ARG cc_start: 0.8559 (mtp-110) cc_final: 0.8074 (ttt90) REVERT: C 552 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7518 (mm) REVERT: C 554 MET cc_start: 0.8192 (mmm) cc_final: 0.7910 (mmp) REVERT: C 652 TYR cc_start: 0.5746 (t80) cc_final: 0.5126 (t80) REVERT: D 651 MET cc_start: 0.7860 (ttp) cc_final: 0.7632 (ttt) outliers start: 26 outliers final: 14 residues processed: 120 average time/residue: 0.1879 time to fit residues: 29.0699 Evaluate side-chains 115 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain D residue 545 TYR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6485 Z= 0.179 Angle : 0.502 6.911 8798 Z= 0.260 Chirality : 0.038 0.172 1032 Planarity : 0.003 0.030 1033 Dihedral : 7.337 76.312 874 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.95 % Allowed : 24.58 % Favored : 71.47 % 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: 1.77 (0.32), residues: 752 helix: 1.41 (0.21), residues: 641 sheet: None (None), residues: 0 loop : 0.12 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.002 0.001 HIS D 562 PHE 0.017 0.001 PHE C 656 TYR 0.017 0.002 TYR B 616 ARG 0.006 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.711 Fit side-chains REVERT: A 576 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 597 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: B 488 ARG cc_start: 0.2315 (OUTLIER) cc_final: 0.1669 (ppt170) REVERT: B 499 LEU cc_start: 0.7329 (pt) cc_final: 0.6991 (pp) REVERT: B 530 LEU cc_start: 0.8859 (mt) cc_final: 0.8503 (mp) REVERT: B 573 ASN cc_start: 0.8935 (t0) cc_final: 0.8578 (t0) REVERT: B 633 ASN cc_start: 0.8982 (t0) cc_final: 0.8578 (t0) REVERT: C 528 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8058 (ttt90) REVERT: C 552 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7463 (mm) REVERT: C 554 MET cc_start: 0.8200 (mmm) cc_final: 0.7900 (mmp) REVERT: C 651 MET cc_start: 0.8631 (tpp) cc_final: 0.8351 (tpp) REVERT: C 652 TYR cc_start: 0.5761 (t80) cc_final: 0.5077 (t80) REVERT: C 655 ILE cc_start: 0.7357 (mt) cc_final: 0.6828 (mt) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.2061 time to fit residues: 30.5938 Evaluate side-chains 116 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 545 TYR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.0060 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6485 Z= 0.193 Angle : 0.504 6.918 8798 Z= 0.261 Chirality : 0.039 0.174 1032 Planarity : 0.003 0.028 1033 Dihedral : 7.357 77.153 874 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.64 % Allowed : 24.58 % Favored : 71.78 % 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: 1.73 (0.32), residues: 752 helix: 1.39 (0.21), residues: 641 sheet: None (None), residues: 0 loop : 0.10 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 568 HIS 0.003 0.001 HIS D 562 PHE 0.015 0.001 PHE C 656 TYR 0.017 0.002 TYR B 616 ARG 0.006 0.000 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.724 Fit side-chains REVERT: A 576 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 597 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: B 488 ARG cc_start: 0.2208 (OUTLIER) cc_final: 0.1546 (ppt170) REVERT: B 499 LEU cc_start: 0.7336 (pt) cc_final: 0.7000 (pp) REVERT: B 530 LEU cc_start: 0.8854 (mt) cc_final: 0.8504 (mp) REVERT: B 573 ASN cc_start: 0.8938 (t0) cc_final: 0.8576 (t0) REVERT: B 633 ASN cc_start: 0.8984 (t0) cc_final: 0.8588 (t0) REVERT: C 528 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.8027 (ttt90) REVERT: C 552 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7477 (mm) REVERT: C 554 MET cc_start: 0.8247 (mmm) cc_final: 0.7956 (mmp) REVERT: C 651 MET cc_start: 0.8523 (tpp) cc_final: 0.8312 (tpp) REVERT: C 652 TYR cc_start: 0.5748 (t80) cc_final: 0.5084 (t80) REVERT: C 655 ILE cc_start: 0.7387 (mt) cc_final: 0.6780 (mt) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.2073 time to fit residues: 29.8784 Evaluate side-chains 115 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain D residue 545 TYR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 647 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6485 Z= 0.207 Angle : 0.519 6.963 8798 Z= 0.269 Chirality : 0.039 0.172 1032 Planarity : 0.003 0.031 1033 Dihedral : 7.397 78.931 874 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.95 % Allowed : 24.28 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.31), residues: 752 helix: 1.78 (0.21), residues: 599 sheet: None (None), residues: 0 loop : 1.03 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 568 HIS 0.003 0.001 HIS D 562 PHE 0.015 0.001 PHE C 656 TYR 0.018 0.002 TYR B 616 ARG 0.006 0.000 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.674 Fit side-chains REVERT: A 576 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 597 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: B 488 ARG cc_start: 0.2263 (OUTLIER) cc_final: 0.1607 (ppt170) REVERT: B 499 LEU cc_start: 0.7300 (pt) cc_final: 0.6969 (pp) REVERT: B 530 LEU cc_start: 0.8871 (mt) cc_final: 0.8528 (mp) REVERT: B 633 ASN cc_start: 0.8983 (t0) cc_final: 0.8598 (t0) REVERT: C 528 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8197 (mtt90) REVERT: C 552 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7473 (mm) REVERT: C 652 TYR cc_start: 0.5847 (t80) cc_final: 0.5152 (t80) REVERT: C 655 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6705 (mt) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.2062 time to fit residues: 30.3549 Evaluate side-chains 119 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 545 TYR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 647 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 0.0020 chunk 70 optimal weight: 0.0060 chunk 46 optimal weight: 0.0470 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6485 Z= 0.138 Angle : 0.487 6.951 8798 Z= 0.247 Chirality : 0.037 0.171 1032 Planarity : 0.003 0.033 1033 Dihedral : 7.203 76.321 874 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.58 % Allowed : 26.25 % Favored : 71.17 % 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: 1.83 (0.32), residues: 752 helix: 1.48 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -0.00 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 568 HIS 0.001 0.000 HIS C 492 PHE 0.013 0.001 PHE B 656 TYR 0.015 0.001 TYR B 652 ARG 0.007 0.000 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.609 Fit side-chains REVERT: A 576 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 488 ARG cc_start: 0.2094 (OUTLIER) cc_final: 0.1467 (ppt170) REVERT: B 499 LEU cc_start: 0.7383 (pt) cc_final: 0.7058 (pp) REVERT: B 530 LEU cc_start: 0.8857 (mt) cc_final: 0.8515 (mp) REVERT: B 633 ASN cc_start: 0.8909 (t0) cc_final: 0.8510 (t0) REVERT: C 528 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8165 (mtt90) REVERT: C 552 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7496 (mm) REVERT: C 554 MET cc_start: 0.8250 (mmm) cc_final: 0.8033 (mmp) REVERT: C 652 TYR cc_start: 0.5836 (t80) cc_final: 0.5443 (t80) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 0.1943 time to fit residues: 28.8308 Evaluate side-chains 114 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 616 TYR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 545 TYR Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6485 Z= 0.175 Angle : 0.523 7.261 8798 Z= 0.267 Chirality : 0.040 0.381 1032 Planarity : 0.003 0.037 1033 Dihedral : 7.082 79.800 872 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.12 % Allowed : 27.16 % Favored : 70.71 % 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: 1.80 (0.32), residues: 752 helix: 1.47 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -0.12 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.002 0.000 HIS D 562 PHE 0.014 0.001 PHE C 656 TYR 0.017 0.002 TYR B 616 ARG 0.008 0.001 ARG B 665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.672 Fit side-chains REVERT: A 576 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 488 ARG cc_start: 0.2160 (OUTLIER) cc_final: 0.1456 (ppt170) REVERT: B 499 LEU cc_start: 0.7319 (pt) cc_final: 0.6993 (pp) REVERT: B 530 LEU cc_start: 0.8859 (mt) cc_final: 0.8521 (mp) REVERT: B 633 ASN cc_start: 0.8963 (t0) cc_final: 0.8554 (t0) REVERT: C 528 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8212 (mtt90) REVERT: C 552 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7479 (mm) outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 0.2124 time to fit residues: 30.4242 Evaluate side-chains 115 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 545 TYR Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.190679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132133 restraints weight = 7718.955| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.05 r_work: 0.3287 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6485 Z= 0.171 Angle : 0.519 7.462 8798 Z= 0.266 Chirality : 0.039 0.305 1032 Planarity : 0.003 0.037 1033 Dihedral : 7.103 79.537 872 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.43 % Allowed : 27.31 % Favored : 70.26 % 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: 1.79 (0.32), residues: 752 helix: 1.46 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -0.08 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 568 HIS 0.002 0.001 HIS D 562 PHE 0.013 0.001 PHE C 656 TYR 0.016 0.002 TYR B 616 ARG 0.008 0.000 ARG B 665 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.96 seconds wall clock time: 37 minutes 55.08 seconds (2275.08 seconds total)