Starting phenix.real_space_refine on Fri Apr 5 16:50:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/04_2024/7wqw_32714.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/04_2024/7wqw_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_32714/04_2024/7wqw_32714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/04_2024/7wqw_32714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/04_2024/7wqw_32714.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wqw_32714/04_2024/7wqw_32714.pdb" } resolution = 3.2 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= 0.020 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 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. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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 dihedrals: 15 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.76, per 1000 atoms: 0.69 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: 1.74 Conformation dependent library (CDL) restraints added in 651.0 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: 0.34 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: 1.07 Time building geometry restraints manager: 1.90 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=" C1 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG A 805 " pdb=" O5 NAG A 805 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG B1104 " pdb=" O5 NAG B1104 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (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: 2391 16.35 - 32.69: 113 32.69 - 49.04: 28 49.04 - 65.38: 10 65.38 - 81.73: 2 Dihedral angle restraints: 2544 sinusoidal: 1132 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 2541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 416 0.035 - 0.069: 132 0.069 - 0.104: 55 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 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: 0.740 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: 3.600 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4080 Z= 0.165 Angle : 0.488 4.561 5554 Z= 0.249 Chirality : 0.043 0.173 628 Planarity : 0.003 0.029 722 Dihedral : 10.247 81.731 1616 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 % Allowed : 6.59 % Favored : 88.94 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 796 HIS 0.001 0.000 HIS A 665 PHE 0.004 0.001 PHE A 537 TYR 0.003 0.000 TYR B 828 ARG 0.002 0.000 ARG A 624 *********************** 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 : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 THR cc_start: 0.6611 (p) cc_final: 0.6247 (p) REVERT: A 648 PHE cc_start: 0.8536 (t80) cc_final: 0.8301 (t80) REVERT: A 700 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.4602 (p90) REVERT: B 848 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6981 (m-40) REVERT: B 968 GLN cc_start: 0.7087 (pm20) cc_final: 0.6774 (pt0) outliers start: 19 outliers final: 5 residues processed: 133 average time/residue: 0.2048 time to fit residues: 32.3558 Evaluate side-chains 71 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 768 ASN A 769 HIS ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 HIS B 921 GLN B 938 ASN B 944 GLN ** B 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4080 Z= 0.154 Angle : 0.539 5.678 5554 Z= 0.278 Chirality : 0.044 0.171 628 Planarity : 0.004 0.030 722 Dihedral : 7.195 57.733 728 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.47 % Allowed : 14.82 % Favored : 80.71 % 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: -3.70 (0.34), residues: 492 helix: -1.84 (0.71), residues: 38 sheet: -2.30 (0.39), residues: 145 loop : -2.73 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1013 HIS 0.019 0.002 HIS A 636 PHE 0.013 0.001 PHE B1017 TYR 0.010 0.001 TYR B 993 ARG 0.004 0.001 ARG B 940 *********************** 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 86 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 535 THR cc_start: 0.7006 (p) cc_final: 0.6593 (p) REVERT: A 648 PHE cc_start: 0.8472 (t80) cc_final: 0.8220 (t80) REVERT: A 693 PHE cc_start: 0.8635 (m-80) cc_final: 0.8153 (m-80) REVERT: A 700 HIS cc_start: 0.5784 (OUTLIER) cc_final: 0.4162 (p90) REVERT: A 750 ILE cc_start: 0.8330 (mp) cc_final: 0.7966 (tt) REVERT: B 848 ASN cc_start: 0.7474 (OUTLIER) cc_final: 0.7010 (m-40) outliers start: 19 outliers final: 9 residues processed: 83 average time/residue: 0.1977 time to fit residues: 19.7535 Evaluate side-chains 66 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0170 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1024 ------------------------------------------------------------------------------- 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 968 GLN B 978 GLN ** B 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4080 Z= 0.298 Angle : 0.607 5.859 5554 Z= 0.312 Chirality : 0.047 0.167 628 Planarity : 0.004 0.043 722 Dihedral : 7.040 59.521 727 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.24 % Allowed : 16.24 % Favored : 79.53 % 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: -3.42 (0.35), residues: 492 helix: -1.40 (0.81), residues: 38 sheet: -2.66 (0.35), residues: 159 loop : -2.19 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 983 HIS 0.003 0.001 HIS B 825 PHE 0.014 0.002 PHE A 681 TYR 0.015 0.002 TYR B 868 ARG 0.003 0.001 ARG B 982 *********************** 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 79 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.483 Fit side-chains REVERT: A 693 PHE cc_start: 0.8751 (m-80) cc_final: 0.8381 (m-80) REVERT: A 705 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6878 (mm-30) REVERT: A 717 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: A 750 ILE cc_start: 0.8455 (mp) cc_final: 0.8099 (tt) REVERT: A 772 CYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5602 (t) REVERT: B 848 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7316 (m-40) REVERT: B 873 LYS cc_start: 0.8388 (mttt) cc_final: 0.8180 (mttt) REVERT: B 952 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7499 (pp20) outliers start: 18 outliers final: 8 residues processed: 76 average time/residue: 0.1753 time to fit residues: 16.4705 Evaluate side-chains 65 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 0.0770 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4080 Z= 0.214 Angle : 0.550 5.454 5554 Z= 0.282 Chirality : 0.045 0.208 628 Planarity : 0.004 0.036 722 Dihedral : 6.620 58.487 723 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.18 % Allowed : 15.76 % Favored : 79.06 % 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: -3.12 (0.35), residues: 492 helix: -1.03 (0.85), residues: 38 sheet: -2.45 (0.36), residues: 155 loop : -2.03 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 983 HIS 0.003 0.001 HIS A 636 PHE 0.020 0.001 PHE A 681 TYR 0.012 0.001 TYR B 803 ARG 0.002 0.000 ARG A 692 *********************** 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 76 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 681 PHE cc_start: 0.7304 (t80) cc_final: 0.6958 (t80) REVERT: A 693 PHE cc_start: 0.8781 (m-80) cc_final: 0.8450 (m-80) REVERT: A 717 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: A 750 ILE cc_start: 0.8363 (mp) cc_final: 0.7985 (tt) REVERT: A 772 CYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5960 (t) REVERT: B 848 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7283 (m-40) REVERT: B 952 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7425 (pp20) outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.1715 time to fit residues: 14.5131 Evaluate side-chains 63 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 845 MET Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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** B 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4080 Z= 0.296 Angle : 0.580 5.578 5554 Z= 0.300 Chirality : 0.046 0.193 628 Planarity : 0.005 0.078 722 Dihedral : 6.779 58.781 721 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 3.76 % Allowed : 16.24 % Favored : 80.00 % 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: -3.06 (0.35), residues: 492 helix: -0.97 (0.86), residues: 38 sheet: -2.42 (0.36), residues: 155 loop : -1.97 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 796 HIS 0.003 0.001 HIS A 636 PHE 0.015 0.002 PHE A 681 TYR 0.009 0.001 TYR B 868 ARG 0.002 0.000 ARG A 692 *********************** 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 64 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8464 (t80) cc_final: 0.8229 (t80) REVERT: A 693 PHE cc_start: 0.8819 (m-80) cc_final: 0.8492 (m-80) REVERT: A 717 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: A 750 ILE cc_start: 0.8342 (mp) cc_final: 0.7953 (tt) REVERT: A 772 CYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5906 (t) REVERT: B 848 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7289 (m-40) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.1750 time to fit residues: 13.6337 Evaluate side-chains 54 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS 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: 1.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 34 optimal weight: 0.0770 overall best weight: 0.8342 ------------------------------------------------------------------------------- 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: 0.7739 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4080 Z= 0.233 Angle : 0.561 5.737 5554 Z= 0.292 Chirality : 0.046 0.196 628 Planarity : 0.004 0.066 722 Dihedral : 6.583 58.476 721 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 4.24 % Allowed : 16.47 % Favored : 79.29 % 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: -2.95 (0.35), residues: 492 helix: -0.87 (0.87), residues: 38 sheet: -2.30 (0.37), residues: 147 loop : -1.96 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 796 HIS 0.003 0.001 HIS A 636 PHE 0.011 0.001 PHE A 606 TYR 0.007 0.001 TYR B 803 ARG 0.001 0.000 ARG A 692 *********************** 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 65 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8448 (t80) cc_final: 0.8218 (t80) REVERT: A 693 PHE cc_start: 0.8853 (m-80) cc_final: 0.8537 (m-80) REVERT: A 717 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: A 750 ILE cc_start: 0.8352 (mp) cc_final: 0.7965 (tt) REVERT: A 772 CYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5787 (t) REVERT: B 848 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7346 (m-40) outliers start: 18 outliers final: 9 residues processed: 64 average time/residue: 0.1680 time to fit residues: 13.4748 Evaluate side-chains 55 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4080 Z= 0.330 Angle : 0.611 5.917 5554 Z= 0.318 Chirality : 0.047 0.188 628 Planarity : 0.005 0.063 722 Dihedral : 7.032 58.868 721 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 3.76 % Allowed : 17.41 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.36), residues: 492 helix: -1.04 (0.83), residues: 38 sheet: -2.65 (0.37), residues: 142 loop : -1.79 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 707 HIS 0.003 0.001 HIS A 636 PHE 0.017 0.002 PHE A 681 TYR 0.008 0.001 TYR B 868 ARG 0.003 0.000 ARG A 692 *********************** 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 66 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8456 (t80) cc_final: 0.8227 (t80) REVERT: A 693 PHE cc_start: 0.8832 (m-80) cc_final: 0.8507 (m-80) REVERT: A 717 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: A 750 ILE cc_start: 0.8384 (mp) cc_final: 0.7988 (tt) REVERT: A 772 CYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5854 (t) REVERT: B 884 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7527 (m-80) outliers start: 16 outliers final: 9 residues processed: 64 average time/residue: 0.1746 time to fit residues: 14.0328 Evaluate side-chains 56 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 0.0040 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 0.3550 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4080 Z= 0.160 Angle : 0.556 5.541 5554 Z= 0.291 Chirality : 0.045 0.208 628 Planarity : 0.004 0.057 722 Dihedral : 6.447 59.388 721 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.29 % Allowed : 19.06 % Favored : 77.65 % 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: -0.69 (0.88), residues: 38 sheet: -2.17 (0.38), residues: 147 loop : -1.86 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 915 HIS 0.004 0.001 HIS A 769 PHE 0.012 0.001 PHE A 606 TYR 0.015 0.001 TYR A 546 ARG 0.001 0.000 ARG B 870 *********************** 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 61 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8860 (m-80) cc_final: 0.8532 (m-10) REVERT: A 717 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: A 750 ILE cc_start: 0.8326 (mp) cc_final: 0.7967 (tt) REVERT: A 772 CYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5818 (t) REVERT: B 848 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7427 (m-40) REVERT: B 884 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7431 (m-80) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.1712 time to fit residues: 13.2369 Evaluate side-chains 60 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS 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: 1.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4080 Z= 0.288 Angle : 0.604 5.719 5554 Z= 0.316 Chirality : 0.047 0.188 628 Planarity : 0.005 0.059 722 Dihedral : 6.868 59.361 721 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 4.00 % Allowed : 18.35 % Favored : 77.65 % 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: -2.80 (0.37), residues: 492 helix: -0.84 (0.86), residues: 38 sheet: -2.21 (0.38), residues: 148 loop : -1.84 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 983 HIS 0.005 0.001 HIS A 769 PHE 0.012 0.001 PHE A 537 TYR 0.009 0.002 TYR B 993 ARG 0.003 0.000 ARG A 679 *********************** 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 65 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8466 (t80) cc_final: 0.8238 (t80) REVERT: A 693 PHE cc_start: 0.8833 (m-80) cc_final: 0.8476 (m-80) REVERT: A 717 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: A 750 ILE cc_start: 0.8345 (mp) cc_final: 0.7974 (tt) REVERT: A 772 CYS cc_start: 0.6258 (OUTLIER) cc_final: 0.6000 (t) REVERT: B 872 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7223 (mtt180) outliers start: 17 outliers final: 12 residues processed: 63 average time/residue: 0.1562 time to fit residues: 12.5735 Evaluate side-chains 64 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4080 Z= 0.185 Angle : 0.575 5.845 5554 Z= 0.303 Chirality : 0.045 0.199 628 Planarity : 0.004 0.059 722 Dihedral : 6.537 59.516 721 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.82 % Allowed : 19.29 % Favored : 77.88 % 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: -2.75 (0.36), residues: 492 helix: -0.69 (0.87), residues: 38 sheet: -2.13 (0.38), residues: 149 loop : -1.84 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 915 HIS 0.004 0.001 HIS A 769 PHE 0.010 0.001 PHE A 606 TYR 0.018 0.001 TYR B 803 ARG 0.001 0.000 ARG A 679 ********************** 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 59 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8387 (t80) cc_final: 0.8157 (t80) REVERT: A 693 PHE cc_start: 0.8839 (m-80) cc_final: 0.8476 (m-10) REVERT: A 717 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: A 750 ILE cc_start: 0.8413 (mp) cc_final: 0.7984 (tt) REVERT: A 772 CYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5853 (t) REVERT: B 848 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7457 (m-40) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.1665 time to fit residues: 12.0782 Evaluate side-chains 57 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.0000 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.3342 ------------------------------------------------------------------------------- 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 ** 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 = 0.3944 r_free = 0.3944 target = 0.133078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097788 restraints weight = 6430.352| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.10 r_work: 0.3310 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4080 Z= 0.159 Angle : 0.559 5.497 5554 Z= 0.294 Chirality : 0.045 0.208 628 Planarity : 0.004 0.059 722 Dihedral : 6.379 59.021 721 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.82 % Allowed : 19.06 % Favored : 78.12 % 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: -2.58 (0.36), residues: 492 helix: -0.63 (0.87), residues: 38 sheet: -1.89 (0.41), residues: 139 loop : -1.82 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 915 HIS 0.003 0.001 HIS A 769 PHE 0.019 0.001 PHE A 681 TYR 0.015 0.001 TYR B 803 ARG 0.001 0.000 ARG B 870 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1430.17 seconds wall clock time: 26 minutes 41.91 seconds (1601.91 seconds total)