Starting phenix.real_space_refine (version: dev) on Fri Feb 17 07:42:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/02_2023/7wqw_32714.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/02_2023/7wqw_32714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/02_2023/7wqw_32714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/02_2023/7wqw_32714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/02_2023/7wqw_32714.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/02_2023/7wqw_32714.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3983 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2013 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 15, 'TRANS': 245} Chain: "B" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.66, per 1000 atoms: 0.67 Number of scatterers: 3983 At special positions: 0 Unit cell: (64.852, 86.818, 96.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 775 8.00 N 678 7.00 C 2501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS B 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 977 " distance=2.03 Simple disulfide: pdb=" SG CYS B 941 " - pdb=" SG CYS B 956 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 995 " 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 725 " " NAG A 802 " - " ASN A 706 " " NAG A 803 " - " ASN A 682 " " NAG A 804 " - " ASN A 630 " " NAG A 805 " - " ASN A 534 " " NAG B1101 " - " ASN B 949 " " NAG B1102 " - " ASN B 909 " " NAG B1103 " - " ASN B 887 " " NAG B1104 " - " ASN B 848 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 746.1 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 7.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.550A pdb=" N GLU A 674 " --> pdb=" O GLY A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 1010 through 1019 removed outlier: 4.079A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 538 removed outlier: 3.565A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 557 removed outlier: 3.569A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 616 " --> pdb=" O CYS A 552 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 614 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA4, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 703 removed outlier: 4.693A pdb=" N LEU A 741 " --> pdb=" O CYS A 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 740 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 752 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 750 " --> pdb=" O ASN A 742 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.586A pdb=" N GLN B 929 " --> pdb=" O GLY B 914 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN B 909 " --> pdb=" O GLN B 978 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN B 978 " --> pdb=" O ASN B 909 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 913 " --> pdb=" O PRO B 974 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 987 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N CYS B 977 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU B 985 " --> pdb=" O CYS B 977 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL B1003 " --> pdb=" O SER B 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 799 through 804 removed outlier: 3.612A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 210 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: 1.05 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1312 1.34 - 1.46: 901 1.46 - 1.58: 1831 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4080 Sorted by residual: bond pdb=" CA GLY B 922 " pdb=" C GLY B 922 " ideal model delta sigma weight residual 1.514 1.503 0.011 1.41e-02 5.03e+03 5.89e-01 bond pdb=" CA GLY B 811 " pdb=" C GLY B 811 " ideal model delta sigma weight residual 1.514 1.523 -0.008 1.41e-02 5.03e+03 3.59e-01 bond pdb=" C GLY B 811 " pdb=" O GLY B 811 " ideal model delta sigma weight residual 1.235 1.227 0.008 1.35e-02 5.49e+03 3.49e-01 bond pdb=" CA GLY A 683 " pdb=" C GLY A 683 " ideal model delta sigma weight residual 1.518 1.514 0.004 7.30e-03 1.88e+04 3.47e-01 bond pdb=" C PHE A 542 " pdb=" N PRO A 543 " ideal model delta sigma weight residual 1.334 1.343 -0.009 1.51e-02 4.39e+03 3.47e-01 ... (remaining 4075 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 193 107.38 - 114.04: 2284 114.04 - 120.69: 1442 120.69 - 127.34: 1579 127.34 - 134.00: 56 Bond angle restraints: 5554 Sorted by residual: angle pdb=" N GLY A 585 " pdb=" CA GLY A 585 " pdb=" C GLY A 585 " ideal model delta sigma weight residual 113.18 117.25 -4.07 2.37e+00 1.78e-01 2.96e+00 angle pdb=" C ASN A 575 " pdb=" N ILE A 576 " pdb=" CA ILE A 576 " ideal model delta sigma weight residual 120.62 123.15 -2.53 1.64e+00 3.72e-01 2.38e+00 angle pdb=" C ASN A 682 " pdb=" N GLY A 683 " pdb=" CA GLY A 683 " ideal model delta sigma weight residual 122.80 121.37 1.43 9.70e-01 1.06e+00 2.19e+00 angle pdb=" CA GLN A 759 " pdb=" CB GLN A 759 " pdb=" CG GLN A 759 " ideal model delta sigma weight residual 114.10 117.04 -2.94 2.00e+00 2.50e-01 2.16e+00 angle pdb=" NE ARG B 830 " pdb=" CZ ARG B 830 " pdb=" NH1 ARG B 830 " ideal model delta sigma weight residual 121.50 120.05 1.45 1.00e+00 1.00e+00 2.11e+00 ... (remaining 5549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2275 16.35 - 32.69: 102 32.69 - 49.04: 24 49.04 - 65.38: 6 65.38 - 81.73: 2 Dihedral angle restraints: 2409 sinusoidal: 997 harmonic: 1412 Sorted by residual: dihedral pdb=" CA SER A 539 " pdb=" C SER A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" N ASN B 848 " pdb=" CA ASN B 848 " pdb=" CB ASN B 848 " pdb=" CG ASN B 848 " ideal model delta sinusoidal sigma weight residual -180.00 -121.53 -58.47 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N CYS A 662 " pdb=" CA CYS A 662 " pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " ideal model delta sinusoidal sigma weight residual -60.00 -117.30 57.30 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 433 0.035 - 0.069: 124 0.069 - 0.104: 46 0.104 - 0.138: 24 0.138 - 0.173: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" C1 NAG A 804 " pdb=" ND2 ASN A 630 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA VAL B 919 " pdb=" N VAL B 919 " pdb=" C VAL B 919 " pdb=" CB VAL B 919 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE B 862 " pdb=" N ILE B 862 " pdb=" C ILE B 862 " pdb=" CB ILE B 862 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 625 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 542 " -0.020 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO A 543 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 527 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 532 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.54e-01 pdb=" N PRO A 533 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.014 5.00e-02 4.00e+02 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1028 2.80 - 3.32: 3674 3.32 - 3.85: 6640 3.85 - 4.37: 7574 4.37 - 4.90: 12826 Nonbonded interactions: 31742 Sorted by model distance: nonbonded pdb=" OD1 ASP A 584 " pdb=" OG1 THR A 609 " model vdw 2.272 2.440 nonbonded pdb=" OD1 ASP B 874 " pdb=" OG1 THR B 951 " model vdw 2.306 2.440 nonbonded pdb=" OD2 ASP A 584 " pdb=" OG1 THR A 608 " model vdw 2.309 2.440 nonbonded pdb=" OD2 ASP B 874 " pdb=" ND2 ASN B 875 " model vdw 2.319 2.520 nonbonded pdb=" NZ LYS A 740 " pdb=" O SER A 754 " model vdw 2.359 2.520 ... (remaining 31737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2501 2.51 5 N 678 2.21 5 O 775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.120 Check model and map are aligned: 0.050 Process input model: 15.250 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.002 0.017 4080 Z= 0.100 Angle : 0.430 4.561 5554 Z= 0.238 Chirality : 0.041 0.173 628 Planarity : 0.003 0.029 722 Dihedral : 9.937 81.731 1481 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 4.47 % 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: -4.30 (0.31), residues: 492 helix: -2.87 (0.53), residues: 36 sheet: -2.55 (0.41), residues: 127 loop : -3.18 (0.29), residues: 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 133 average time/residue: 0.2237 time to fit residues: 35.1458 Evaluate side-chains 70 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0392 time to fit residues: 0.9597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.0030 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 HIS B 921 GLN B 944 GLN ** B 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4080 Z= 0.269 Angle : 0.589 5.349 5554 Z= 0.310 Chirality : 0.046 0.256 628 Planarity : 0.004 0.033 722 Dihedral : 4.281 16.731 582 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer Outliers : 3.06 % 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: -3.77 (0.34), residues: 492 helix: -1.79 (0.74), residues: 38 sheet: -2.52 (0.38), residues: 150 loop : -2.69 (0.33), residues: 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.497 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.2007 time to fit residues: 19.1800 Evaluate side-chains 59 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0609 time to fit residues: 1.7598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 4080 Z= 0.395 Angle : 0.634 6.236 5554 Z= 0.334 Chirality : 0.048 0.208 628 Planarity : 0.004 0.034 722 Dihedral : 4.770 23.214 582 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer Outliers : 3.29 % 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: -3.40 (0.36), residues: 492 helix: -1.56 (0.80), residues: 38 sheet: -2.64 (0.38), residues: 157 loop : -2.15 (0.35), residues: 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.514 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 71 average time/residue: 0.1821 time to fit residues: 16.1101 Evaluate side-chains 55 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1061 time to fit residues: 1.3276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4080 Z= 0.225 Angle : 0.550 5.380 5554 Z= 0.291 Chirality : 0.045 0.207 628 Planarity : 0.005 0.072 722 Dihedral : 4.589 19.210 582 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 2.12 % 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: -3.17 (0.36), residues: 492 helix: -1.37 (0.84), residues: 38 sheet: -2.39 (0.37), residues: 149 loop : -2.10 (0.35), residues: 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.503 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.1887 time to fit residues: 13.8161 Evaluate side-chains 51 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0477 time to fit residues: 1.1392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 4080 Z= 0.266 Angle : 0.560 5.672 5554 Z= 0.296 Chirality : 0.045 0.219 628 Planarity : 0.004 0.061 722 Dihedral : 4.708 20.953 582 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.36), residues: 492 helix: -1.27 (0.84), residues: 38 sheet: -2.50 (0.37), residues: 154 loop : -1.86 (0.36), residues: 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.514 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 58 average time/residue: 0.1978 time to fit residues: 14.1783 Evaluate side-chains 46 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.0000 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4080 Z= 0.207 Angle : 0.555 5.510 5554 Z= 0.294 Chirality : 0.045 0.230 628 Planarity : 0.004 0.058 722 Dihedral : 4.602 17.526 582 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer Outliers : 2.12 % 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: -2.95 (0.36), residues: 492 helix: -1.21 (0.84), residues: 38 sheet: -2.36 (0.37), residues: 147 loop : -1.87 (0.35), residues: 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.458 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 60 average time/residue: 0.1642 time to fit residues: 12.5961 Evaluate side-chains 50 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0434 time to fit residues: 0.8490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4080 Z= 0.226 Angle : 0.564 5.959 5554 Z= 0.299 Chirality : 0.045 0.225 628 Planarity : 0.004 0.056 722 Dihedral : 4.735 19.278 582 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer Outliers : 1.41 % 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: -2.88 (0.36), residues: 492 helix: -1.18 (0.83), residues: 38 sheet: -2.30 (0.38), residues: 147 loop : -1.83 (0.35), residues: 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.490 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 0.1708 time to fit residues: 12.4209 Evaluate side-chains 51 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0512 time to fit residues: 0.8736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4080 Z= 0.215 Angle : 0.567 6.426 5554 Z= 0.301 Chirality : 0.045 0.225 628 Planarity : 0.004 0.056 722 Dihedral : 4.691 16.394 582 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.36), residues: 492 helix: -1.06 (0.82), residues: 38 sheet: -2.21 (0.38), residues: 147 loop : -1.79 (0.35), residues: 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.485 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1965 time to fit residues: 11.9554 Evaluate side-chains 47 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4080 Z= 0.251 Angle : 0.595 6.738 5554 Z= 0.316 Chirality : 0.045 0.206 628 Planarity : 0.004 0.057 722 Dihedral : 4.821 19.060 582 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer Outliers : 0.47 % 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: -2.76 (0.37), residues: 492 helix: -1.04 (0.84), residues: 38 sheet: -2.21 (0.39), residues: 151 loop : -1.74 (0.36), residues: 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.473 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.2071 time to fit residues: 12.9093 Evaluate side-chains 47 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0419 time to fit residues: 0.6982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4080 Z= 0.269 Angle : 0.612 6.997 5554 Z= 0.325 Chirality : 0.046 0.210 628 Planarity : 0.004 0.056 722 Dihedral : 4.914 18.399 582 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.37), residues: 492 helix: -1.03 (0.83), residues: 38 sheet: -2.18 (0.38), residues: 153 loop : -1.82 (0.36), residues: 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.477 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1938 time to fit residues: 11.7912 Evaluate side-chains 46 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.0170 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.131769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096604 restraints weight = 6472.286| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.06 r_work: 0.3286 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4080 Z= 0.183 Angle : 0.585 7.173 5554 Z= 0.311 Chirality : 0.045 0.230 628 Planarity : 0.004 0.055 722 Dihedral : 4.783 16.521 582 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer Outliers : 0.24 % 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: -2.73 (0.37), residues: 492 helix: -0.94 (0.84), residues: 38 sheet: -2.13 (0.39), residues: 152 loop : -1.77 (0.36), residues: 302 =============================================================================== Job complete usr+sys time: 1303.35 seconds wall clock time: 24 minutes 23.36 seconds (1463.36 seconds total)