Starting phenix.real_space_refine on Fri Dec 27 10:17:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqw_32714/12_2024/7wqw_32714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqw_32714/12_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/cci-nas-00/data/ceres_data/7wqw_32714/12_2024/7wqw_32714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqw_32714/12_2024/7wqw_32714.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqw_32714/12_2024/7wqw_32714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqw_32714/12_2024/7wqw_32714.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.99, per 1000 atoms: 0.75 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 0.93 Conformation dependent library (CDL) restraints added in 461.8 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: 0.46 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: 1.03 Time building geometry restraints manager: 1.08 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: 0.00 - 0.91: 5220 0.91 - 1.82: 248 1.82 - 2.74: 72 2.74 - 3.65: 11 3.65 - 4.56: 3 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 3.040 nonbonded pdb=" OD1 ASP B 874 " pdb=" OG1 THR B 951 " model vdw 2.306 3.040 nonbonded pdb=" OD2 ASP A 584 " pdb=" OG1 THR A 608 " model vdw 2.309 3.040 nonbonded pdb=" OD2 ASP B 874 " pdb=" ND2 ASN B 875 " model vdw 2.319 3.120 nonbonded pdb=" NZ LYS A 740 " pdb=" O SER A 754 " model vdw 2.359 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.860 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.435 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: 0.2100 time to fit residues: 33.1449 Evaluate side-chains 71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS A 713 ASN A 769 HIS B 875 ASN B 881 HIS B 921 GLN B 944 GLN B 968 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3036 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= 0.208 Angle : 0.590 5.183 5554 Z= 0.306 Chirality : 0.046 0.182 628 Planarity : 0.004 0.031 722 Dihedral : 7.362 58.186 728 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.94 % Allowed : 14.35 % 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: -3.69 (0.34), residues: 492 helix: -2.03 (0.67), residues: 38 sheet: -2.38 (0.38), residues: 148 loop : -2.64 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 983 HIS 0.019 0.002 HIS A 636 PHE 0.010 0.001 PHE B1017 TYR 0.011 0.001 TYR B 993 ARG 0.007 0.001 ARG A 764 *********************** 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 85 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 THR cc_start: 0.7281 (p) cc_final: 0.6886 (p) REVERT: A 647 HIS cc_start: 0.5959 (m170) cc_final: 0.5694 (m170) REVERT: A 648 PHE cc_start: 0.8488 (t80) cc_final: 0.8220 (t80) REVERT: A 693 PHE cc_start: 0.8706 (m-80) cc_final: 0.8255 (m-80) REVERT: A 700 HIS cc_start: 0.5893 (OUTLIER) cc_final: 0.4107 (p90) REVERT: A 750 ILE cc_start: 0.8317 (mp) cc_final: 0.7958 (tt) REVERT: A 772 CYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6207 (t) REVERT: B 848 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7031 (m-40) REVERT: B 880 MET cc_start: 0.8146 (mtt) cc_final: 0.7924 (mtt) outliers start: 21 outliers final: 10 residues processed: 79 average time/residue: 0.1939 time to fit residues: 18.6838 Evaluate side-chains 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 739 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 CYS 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 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: 0.7980 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 875 ASN B 978 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4080 Z= 0.305 Angle : 0.609 6.234 5554 Z= 0.314 Chirality : 0.048 0.193 628 Planarity : 0.004 0.032 722 Dihedral : 7.357 59.570 726 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 4.94 % Allowed : 15.53 % 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: -3.36 (0.35), residues: 492 helix: -1.44 (0.76), residues: 38 sheet: -2.65 (0.36), residues: 168 loop : -2.06 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 983 HIS 0.003 0.001 HIS A 636 PHE 0.013 0.002 PHE A 681 TYR 0.012 0.001 TYR B 868 ARG 0.003 0.001 ARG A 764 *********************** 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 81 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8350 (pt) REVERT: A 647 HIS cc_start: 0.6115 (m170) cc_final: 0.5891 (m170) REVERT: A 693 PHE cc_start: 0.8782 (m-80) cc_final: 0.8459 (m-80) REVERT: A 700 HIS cc_start: 0.5940 (OUTLIER) cc_final: 0.5127 (p90) REVERT: A 717 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: A 750 ILE cc_start: 0.8338 (mp) cc_final: 0.7982 (tt) REVERT: A 772 CYS cc_start: 0.6329 (OUTLIER) cc_final: 0.6035 (t) REVERT: B 848 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7320 (m-40) REVERT: B 880 MET cc_start: 0.8299 (mtt) cc_final: 0.8035 (mtt) outliers start: 21 outliers final: 11 residues processed: 78 average time/residue: 0.1797 time to fit residues: 17.3922 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 765 LEU 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 951 THR 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: 0.1980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4080 Z= 0.176 Angle : 0.545 5.315 5554 Z= 0.283 Chirality : 0.045 0.205 628 Planarity : 0.005 0.072 722 Dihedral : 6.820 59.224 724 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.18 % Allowed : 16.24 % Favored : 78.59 % 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: -2.97 (0.36), residues: 492 helix: -1.21 (0.77), residues: 38 sheet: -1.96 (0.40), residues: 139 loop : -2.15 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 983 HIS 0.004 0.001 HIS A 636 PHE 0.015 0.001 PHE A 606 TYR 0.008 0.001 TYR B 959 ARG 0.005 0.000 ARG A 679 *********************** 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 77 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6203 (m90) cc_final: 0.5746 (m170) REVERT: A 692 ARG cc_start: 0.7531 (tpp80) cc_final: 0.7092 (mmm160) REVERT: A 693 PHE cc_start: 0.8817 (m-80) cc_final: 0.8327 (m-80) REVERT: A 700 HIS cc_start: 0.5857 (OUTLIER) cc_final: 0.4963 (p90) REVERT: A 717 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: A 750 ILE cc_start: 0.8343 (mp) cc_final: 0.7981 (tt) REVERT: A 762 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7691 (mm) REVERT: A 772 CYS cc_start: 0.6280 (OUTLIER) cc_final: 0.6011 (t) REVERT: B 848 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7270 (m-40) REVERT: B 873 LYS cc_start: 0.8391 (mttt) cc_final: 0.8187 (mttm) REVERT: B 880 MET cc_start: 0.8248 (mtt) cc_final: 0.7973 (mtt) outliers start: 22 outliers final: 11 residues processed: 71 average time/residue: 0.1631 time to fit residues: 14.5302 Evaluate side-chains 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 772 CYS 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 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: 0.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7769 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4080 Z= 0.323 Angle : 0.607 6.048 5554 Z= 0.314 Chirality : 0.047 0.212 628 Planarity : 0.005 0.062 722 Dihedral : 7.230 59.422 724 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.65 % Allowed : 15.76 % Favored : 78.59 % 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: -2.96 (0.36), residues: 492 helix: -1.22 (0.77), residues: 38 sheet: -2.28 (0.41), residues: 133 loop : -1.98 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 983 HIS 0.006 0.001 HIS A 636 PHE 0.021 0.002 PHE A 681 TYR 0.020 0.002 TYR B 803 ARG 0.005 0.001 ARG A 679 *********************** 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 76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6240 (m90) cc_final: 0.6039 (m170) REVERT: A 648 PHE cc_start: 0.8474 (t80) cc_final: 0.8227 (t80) REVERT: A 700 HIS cc_start: 0.6133 (OUTLIER) cc_final: 0.5152 (p90) REVERT: A 717 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: A 750 ILE cc_start: 0.8412 (mp) cc_final: 0.8031 (tt) REVERT: A 779 GLN cc_start: 0.4806 (OUTLIER) cc_final: 0.4533 (mt0) REVERT: B 848 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7274 (m-40) REVERT: B 880 MET cc_start: 0.8361 (mtt) cc_final: 0.8073 (mtt) outliers start: 24 outliers final: 11 residues processed: 73 average time/residue: 0.1736 time to fit residues: 15.7120 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain B residue 800 VAL 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 977 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7734 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4080 Z= 0.219 Angle : 0.576 6.058 5554 Z= 0.299 Chirality : 0.046 0.215 628 Planarity : 0.004 0.058 722 Dihedral : 6.738 59.092 723 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.47 % Allowed : 17.41 % 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: -2.84 (0.36), residues: 492 helix: -1.10 (0.79), residues: 38 sheet: -2.41 (0.39), residues: 138 loop : -1.77 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 983 HIS 0.003 0.001 HIS A 636 PHE 0.011 0.001 PHE A 537 TYR 0.014 0.001 TYR B 803 ARG 0.004 0.000 ARG A 679 *********************** 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 69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8472 (t80) cc_final: 0.8234 (t80) REVERT: A 700 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.5335 (p90) REVERT: A 717 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: A 750 ILE cc_start: 0.8446 (mp) cc_final: 0.8109 (tt) REVERT: A 779 GLN cc_start: 0.4798 (OUTLIER) cc_final: 0.4564 (mt0) REVERT: B 848 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7299 (m-40) REVERT: B 880 MET cc_start: 0.8309 (mtt) cc_final: 0.8045 (mtt) outliers start: 19 outliers final: 11 residues processed: 68 average time/residue: 0.1698 time to fit residues: 14.4034 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 GLN 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 951 THR 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: 0.7980 chunk 47 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 844 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4986 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= 0.230 Angle : 0.591 5.703 5554 Z= 0.306 Chirality : 0.046 0.216 628 Planarity : 0.004 0.056 722 Dihedral : 6.759 59.410 723 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.24 % Allowed : 17.88 % 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 (0.37), residues: 492 helix: -1.00 (0.81), residues: 38 sheet: -2.37 (0.40), residues: 138 loop : -1.70 (0.35), residues: 316 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 0.011 0.001 PHE A 537 TYR 0.016 0.002 TYR B 803 ARG 0.003 0.000 ARG A 679 *********************** 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 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8493 (t80) cc_final: 0.8275 (t80) REVERT: A 700 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.5400 (p90) REVERT: A 717 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: A 750 ILE cc_start: 0.8406 (mp) cc_final: 0.8019 (tt) REVERT: A 779 GLN cc_start: 0.4824 (OUTLIER) cc_final: 0.4561 (mt0) REVERT: B 848 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7305 (m-40) REVERT: B 880 MET cc_start: 0.8327 (mtt) cc_final: 0.8046 (mtt) outliers start: 18 outliers final: 12 residues processed: 66 average time/residue: 0.1719 time to fit residues: 14.1754 Evaluate side-chains 60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 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 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 779 GLN 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 951 THR 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: 0.9980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4982 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= 0.191 Angle : 0.577 5.671 5554 Z= 0.300 Chirality : 0.046 0.219 628 Planarity : 0.004 0.056 722 Dihedral : 6.613 59.453 723 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.06 % Allowed : 19.53 % Favored : 77.41 % 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: -2.64 (0.37), residues: 492 helix: -0.91 (0.82), residues: 38 sheet: -2.27 (0.40), residues: 138 loop : -1.64 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 915 HIS 0.004 0.001 HIS A 636 PHE 0.010 0.001 PHE A 537 TYR 0.015 0.001 TYR B 803 ARG 0.003 0.000 ARG A 679 *********************** 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 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 PHE cc_start: 0.8502 (t80) cc_final: 0.8293 (t80) REVERT: A 700 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5398 (p90) REVERT: A 717 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: A 750 ILE cc_start: 0.8390 (mp) cc_final: 0.8055 (tt) REVERT: A 772 CYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6280 (t) REVERT: A 779 GLN cc_start: 0.4783 (OUTLIER) cc_final: 0.4521 (mt0) REVERT: B 848 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7297 (m-40) REVERT: B 880 MET cc_start: 0.8311 (mtt) cc_final: 0.8048 (mtt) outliers start: 13 outliers final: 7 residues processed: 65 average time/residue: 0.1767 time to fit residues: 14.6936 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 779 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5159 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= 0.232 Angle : 0.601 6.248 5554 Z= 0.314 Chirality : 0.047 0.215 628 Planarity : 0.004 0.056 722 Dihedral : 6.727 59.451 723 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 3.53 % Allowed : 18.12 % Favored : 78.35 % 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: -2.59 (0.37), residues: 492 helix: -0.96 (0.81), residues: 38 sheet: -1.87 (0.41), residues: 137 loop : -1.79 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 983 HIS 0.004 0.001 HIS A 636 PHE 0.011 0.001 PHE A 537 TYR 0.017 0.002 TYR B 803 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 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6020 (m-70) cc_final: 0.5777 (m-70) REVERT: A 648 PHE cc_start: 0.8473 (t80) cc_final: 0.8260 (t80) REVERT: A 700 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5446 (p90) REVERT: A 717 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: A 750 ILE cc_start: 0.8414 (mp) cc_final: 0.8077 (tt) REVERT: A 772 CYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6415 (t) REVERT: A 779 GLN cc_start: 0.4839 (OUTLIER) cc_final: 0.4518 (mt0) REVERT: B 848 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7331 (m-40) REVERT: B 880 MET cc_start: 0.8308 (mtt) cc_final: 0.8016 (mtt) outliers start: 15 outliers final: 9 residues processed: 67 average time/residue: 0.1818 time to fit residues: 15.3834 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 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 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 779 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4080 Z= 0.215 Angle : 0.593 5.675 5554 Z= 0.311 Chirality : 0.046 0.216 628 Planarity : 0.004 0.056 722 Dihedral : 6.691 59.514 723 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 3.29 % Allowed : 18.59 % 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 (0.37), residues: 492 helix: -0.94 (0.82), residues: 38 sheet: -2.02 (0.43), residues: 125 loop : -1.74 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 699 HIS 0.007 0.001 HIS A 636 PHE 0.011 0.001 PHE A 537 TYR 0.016 0.001 TYR B 803 ARG 0.003 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 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6030 (m-70) cc_final: 0.5701 (m-70) REVERT: A 648 PHE cc_start: 0.8490 (t80) cc_final: 0.8279 (t80) REVERT: A 700 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.5440 (p90) REVERT: A 717 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: A 750 ILE cc_start: 0.8387 (mp) cc_final: 0.8032 (tt) REVERT: A 772 CYS cc_start: 0.6464 (OUTLIER) cc_final: 0.6205 (t) REVERT: A 779 GLN cc_start: 0.4825 (OUTLIER) cc_final: 0.4458 (mt0) REVERT: B 848 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7330 (m-40) REVERT: B 880 MET cc_start: 0.8318 (mtt) cc_final: 0.8039 (mtt) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.1775 time to fit residues: 14.3810 Evaluate side-chains 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 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 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 779 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.0010 chunk 26 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.096945 restraints weight = 6371.288| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.13 r_work: 0.3291 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5185 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= 0.173 Angle : 0.588 6.028 5554 Z= 0.309 Chirality : 0.046 0.227 628 Planarity : 0.004 0.055 722 Dihedral : 6.552 59.517 723 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.06 % Allowed : 19.06 % 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: -2.48 (0.37), residues: 492 helix: -1.01 (0.81), residues: 38 sheet: -1.80 (0.42), residues: 137 loop : -1.69 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 915 HIS 0.008 0.001 HIS A 636 PHE 0.010 0.001 PHE A 537 TYR 0.014 0.001 TYR A 546 ARG 0.004 0.000 ARG A 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.36 seconds wall clock time: 25 minutes 43.26 seconds (1543.26 seconds total)