Starting phenix.real_space_refine on Fri Dec 27 12:45:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vti_43523/12_2024/8vti_43523.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vti_43523/12_2024/8vti_43523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vti_43523/12_2024/8vti_43523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vti_43523/12_2024/8vti_43523.map" model { file = "/net/cci-nas-00/data/ceres_data/8vti_43523/12_2024/8vti_43523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vti_43523/12_2024/8vti_43523.cif" } resolution = 3.9 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 66 atoms to isotropic. 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 23 5.16 5 C 2917 2.51 5 N 808 2.21 5 O 919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4667 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2781 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 344} Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "C" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.93, per 1000 atoms: 1.27 Number of scatterers: 4667 At special positions: 0 Unit cell: (79.9085, 98.039, 106.769, 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 23 16.00 O 919 8.00 N 808 7.00 C 2917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 498 " - pdb=" SG CYS A 533 " distance=2.00 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 550 " distance=2.05 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 849 " distance=2.02 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.01 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A 901 " - " ASN A 843 " " NAG E 1 " - " ASN A 817 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 541.6 milliseconds 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 23.3% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 553 through 565 removed outlier: 4.042A pdb=" N HIS A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 3.682A pdb=" N ILE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 609 removed outlier: 3.813A pdb=" N VAL A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 646 removed outlier: 3.522A pdb=" N GLU A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 657 removed outlier: 3.871A pdb=" N TRP A 654 " --> pdb=" O ALA A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 removed outlier: 3.509A pdb=" N ARG A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502 removed outlier: 3.903A pdb=" N ILE A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA4, first strand: chain 'A' and resid 689 through 690 removed outlier: 4.360A pdb=" N ASN B 856 " --> pdb=" O TRP A 821 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 829 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 714 through 715 removed outlier: 3.565A pdb=" N VAL A 801 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 794 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A 852 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 11.251A pdb=" N ASP A 798 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N SER A 850 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N VAL A 800 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N THR A 848 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 10.817A pdb=" N PHE A 802 " --> pdb=" O HIS A 846 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N HIS A 846 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N HIS A 846 " --> pdb=" O THR A 842 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N THR A 842 " --> pdb=" O HIS A 846 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 848 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.640A pdb=" N THR C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.640A pdb=" N THR C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.764A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.100A pdb=" N GLY D 13 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 95 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 561 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: 1.41 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 901 1.33 - 1.45: 1195 1.45 - 1.57: 2633 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 4762 Sorted by residual: bond pdb=" N LYS A 518 " pdb=" CA LYS A 518 " ideal model delta sigma weight residual 1.454 1.503 -0.049 1.29e-02 6.01e+03 1.42e+01 bond pdb=" N ILE A 516 " pdb=" CA ILE A 516 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" N VAL A 775 " pdb=" CA VAL A 775 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" N ILE A 776 " pdb=" CA ILE A 776 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.22e-02 6.72e+03 1.02e+01 bond pdb=" N GLU A 499 " pdb=" CA GLU A 499 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.27e-02 6.20e+03 9.95e+00 ... (remaining 4757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5530 2.26 - 4.53: 917 4.53 - 6.79: 22 6.79 - 9.06: 2 9.06 - 11.32: 1 Bond angle restraints: 6472 Sorted by residual: angle pdb=" C THR A 511 " pdb=" CA THR A 511 " pdb=" CB THR A 511 " ideal model delta sigma weight residual 110.77 122.09 -11.32 1.67e+00 3.59e-01 4.60e+01 angle pdb=" N GLU A 812 " pdb=" CA GLU A 812 " pdb=" C GLU A 812 " ideal model delta sigma weight residual 114.12 106.43 7.69 1.39e+00 5.18e-01 3.06e+01 angle pdb=" C LEU A 645 " pdb=" N LEU A 646 " pdb=" CA LEU A 646 " ideal model delta sigma weight residual 122.73 115.00 7.73 1.61e+00 3.86e-01 2.31e+01 angle pdb=" CA GLN A 515 " pdb=" C GLN A 515 " pdb=" O GLN A 515 " ideal model delta sigma weight residual 121.28 115.81 5.47 1.18e+00 7.18e-01 2.15e+01 angle pdb=" N LEU A 751 " pdb=" CA LEU A 751 " pdb=" C LEU A 751 " ideal model delta sigma weight residual 113.18 107.60 5.58 1.33e+00 5.65e-01 1.76e+01 ... (remaining 6467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 2709 21.25 - 42.50: 153 42.50 - 63.76: 33 63.76 - 85.01: 7 85.01 - 106.26: 5 Dihedral angle restraints: 2907 sinusoidal: 1176 harmonic: 1731 Sorted by residual: dihedral pdb=" CA PHE A 715 " pdb=" C PHE A 715 " pdb=" N PRO A 716 " pdb=" CA PRO A 716 " ideal model delta harmonic sigma weight residual 0.00 -38.08 38.08 0 5.00e+00 4.00e-02 5.80e+01 dihedral pdb=" CA TYR C 95 " pdb=" C TYR C 95 " pdb=" N PRO C 96 " pdb=" CA PRO C 96 " ideal model delta harmonic sigma weight residual 0.00 31.99 -31.99 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" C THR A 511 " pdb=" N THR A 511 " pdb=" CA THR A 511 " pdb=" CB THR A 511 " ideal model delta harmonic sigma weight residual -122.00 -134.78 12.78 0 2.50e+00 1.60e-01 2.61e+01 ... (remaining 2904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 435 0.084 - 0.167: 261 0.167 - 0.250: 44 0.250 - 0.334: 2 0.334 - 0.417: 1 Chirality restraints: 743 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.11e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.16e+01 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 843 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 740 not shown) Planarity restraints: 827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " 0.116 2.00e-02 2.50e+03 9.66e-02 1.17e+02 pdb=" C7 NAG A 901 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " -0.155 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.044 2.00e-02 2.50e+03 3.61e-02 1.63e+01 pdb=" C7 NAG E 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.057 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.042 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" C7 NAG E 1 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.055 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.005 2.00e-02 2.50e+03 ... (remaining 824 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 2411 2.98 - 3.46: 4319 3.46 - 3.94: 7753 3.94 - 4.42: 8548 4.42 - 4.90: 13639 Nonbonded interactions: 36670 Sorted by model distance: nonbonded pdb=" O ASP A 596 " pdb=" OD1 ASP A 596 " model vdw 2.503 3.040 nonbonded pdb=" O GLN C 80 " pdb=" N GLU C 82 " model vdw 2.529 3.120 nonbonded pdb=" OD1 ASP A 615 " pdb=" N ARG A 619 " model vdw 2.547 3.120 nonbonded pdb=" O LEU A 601 " pdb=" OE1 GLN A 605 " model vdw 2.550 3.040 nonbonded pdb=" N PHE A 509 " pdb=" O PHE A 509 " model vdw 2.571 2.496 ... (remaining 36665 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.810 Find NCS groups from input model: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 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 : 0.012 0.049 4762 Z= 0.792 Angle : 1.487 11.324 6472 Z= 1.100 Chirality : 0.094 0.417 743 Planarity : 0.006 0.097 825 Dihedral : 14.581 106.262 1775 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.35 % Favored : 90.48 % Rotamer: Outliers : 3.54 % Allowed : 7.87 % Favored : 88.58 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -3.01 (0.32), residues: 588 helix: 0.12 (0.45), residues: 124 sheet: -2.45 (0.34), residues: 195 loop : -2.62 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 554 HIS 0.004 0.001 HIS A 846 PHE 0.015 0.002 PHE A 745 TYR 0.017 0.002 TYR D 36 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 TYR cc_start: 0.4269 (t80) cc_final: 0.4017 (t80) REVERT: A 554 TRP cc_start: 0.7629 (p90) cc_final: 0.7172 (p90) REVERT: A 573 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7294 (mtm-85) REVERT: A 634 TYR cc_start: 0.7787 (t80) cc_final: 0.7355 (t80) REVERT: A 688 ASP cc_start: 0.8574 (t0) cc_final: 0.7996 (m-30) REVERT: A 701 VAL cc_start: 0.9408 (t) cc_final: 0.8988 (p) REVERT: A 763 LYS cc_start: 0.7409 (ttpt) cc_final: 0.7140 (ttmm) REVERT: A 782 ILE cc_start: 0.8420 (tp) cc_final: 0.8198 (tt) REVERT: A 790 PHE cc_start: 0.8482 (m-80) cc_final: 0.7743 (m-10) REVERT: B 860 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 865 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6758 (mm-30) REVERT: C 24 CYS cc_start: 0.5699 (t) cc_final: 0.5046 (t) REVERT: C 34 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (m) REVERT: C 36 TRP cc_start: 0.8500 (m100) cc_final: 0.8203 (m100) REVERT: C 48 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8368 (mm) REVERT: C 83 ASP cc_start: 0.7748 (t70) cc_final: 0.7469 (t70) REVERT: C 94 GLN cc_start: 0.7723 (pp30) cc_final: 0.6748 (pp30) REVERT: C 104 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6934 (mtpp) REVERT: D 39 TRP cc_start: 0.7896 (m100) cc_final: 0.7251 (m100) REVERT: D 40 VAL cc_start: 0.7922 (t) cc_final: 0.7679 (m) REVERT: D 42 GLN cc_start: 0.7972 (tt0) cc_final: 0.7288 (tt0) REVERT: D 48 LEU cc_start: 0.6942 (mt) cc_final: 0.5852 (mt) REVERT: D 81 THR cc_start: 0.6707 (p) cc_final: 0.6246 (p) REVERT: D 83 TYR cc_start: 0.7883 (m-80) cc_final: 0.7276 (m-80) REVERT: D 87 ASN cc_start: 0.8501 (m-40) cc_final: 0.8171 (m110) REVERT: D 96 VAL cc_start: 0.7433 (t) cc_final: 0.7205 (p) REVERT: D 98 TYR cc_start: 0.6608 (m-80) cc_final: 0.6064 (m-80) REVERT: D 101 ARG cc_start: 0.7492 (tmm160) cc_final: 0.5878 (tmm-80) REVERT: D 107 TRP cc_start: 0.6382 (t60) cc_final: 0.6074 (t60) outliers start: 18 outliers final: 4 residues processed: 217 average time/residue: 0.1943 time to fit residues: 51.1778 Evaluate side-chains 144 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 GLN A 773 HIS C 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4762 Z= 0.233 Angle : 0.681 7.163 6472 Z= 0.354 Chirality : 0.044 0.180 743 Planarity : 0.005 0.046 825 Dihedral : 8.510 79.780 737 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.72 % Allowed : 15.55 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.34), residues: 588 helix: 1.83 (0.43), residues: 129 sheet: -2.10 (0.34), residues: 189 loop : -1.40 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 554 HIS 0.003 0.001 HIS A 773 PHE 0.019 0.002 PHE A 745 TYR 0.029 0.002 TYR C 56 ARG 0.008 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8338 (tpt90) REVERT: A 605 GLN cc_start: 0.8770 (mp10) cc_final: 0.8469 (tp-100) REVERT: A 688 ASP cc_start: 0.8509 (t0) cc_final: 0.7796 (m-30) REVERT: A 719 MET cc_start: 0.8248 (mmm) cc_final: 0.7451 (mpp) REVERT: A 743 VAL cc_start: 0.9363 (t) cc_final: 0.9157 (m) REVERT: A 790 PHE cc_start: 0.8151 (m-80) cc_final: 0.7367 (m-80) REVERT: A 826 ARG cc_start: 0.9325 (ptp90) cc_final: 0.9016 (ptp90) REVERT: B 861 MET cc_start: 0.6598 (tpp) cc_final: 0.6184 (mmm) REVERT: B 865 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6654 (mm-30) REVERT: C 36 TRP cc_start: 0.8928 (m100) cc_final: 0.7578 (m100) REVERT: C 90 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 94 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6688 (pp30) REVERT: C 104 LYS cc_start: 0.6626 (mtpt) cc_final: 0.6422 (mtpp) REVERT: D 39 TRP cc_start: 0.8242 (m100) cc_final: 0.7470 (m100) REVERT: D 42 GLN cc_start: 0.8207 (tt0) cc_final: 0.7981 (tt0) REVERT: D 48 LEU cc_start: 0.8160 (mt) cc_final: 0.7494 (mt) REVERT: D 87 ASN cc_start: 0.8308 (m-40) cc_final: 0.7893 (m-40) REVERT: D 92 GLU cc_start: 0.8630 (mp0) cc_final: 0.8278 (mp0) REVERT: D 93 ASP cc_start: 0.8371 (m-30) cc_final: 0.8126 (m-30) REVERT: D 101 ARG cc_start: 0.7211 (tmm160) cc_final: 0.6022 (tmm-80) outliers start: 24 outliers final: 16 residues processed: 146 average time/residue: 0.1835 time to fit residues: 33.2291 Evaluate side-chains 125 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 110 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN A 671 HIS C 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 4762 Z= 0.356 Angle : 0.720 7.808 6472 Z= 0.378 Chirality : 0.044 0.188 743 Planarity : 0.005 0.047 825 Dihedral : 6.694 78.413 728 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 6.50 % Allowed : 16.54 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.35), residues: 588 helix: 1.95 (0.46), residues: 129 sheet: -1.81 (0.35), residues: 186 loop : -1.51 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 654 HIS 0.004 0.001 HIS D 102 PHE 0.022 0.002 PHE A 509 TYR 0.033 0.003 TYR A 634 ARG 0.005 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8814 (mp10) cc_final: 0.8379 (tp-100) REVERT: A 634 TYR cc_start: 0.8039 (t80) cc_final: 0.7641 (t80) REVERT: A 651 LEU cc_start: 0.8147 (pp) cc_final: 0.7722 (pp) REVERT: A 688 ASP cc_start: 0.8503 (t0) cc_final: 0.7771 (m-30) REVERT: A 719 MET cc_start: 0.8412 (mmm) cc_final: 0.7447 (mpp) REVERT: A 790 PHE cc_start: 0.8289 (m-80) cc_final: 0.7353 (m-10) REVERT: B 861 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6221 (mmm) REVERT: C 13 SER cc_start: 0.3460 (OUTLIER) cc_final: 0.2820 (p) REVERT: C 36 TRP cc_start: 0.9174 (m100) cc_final: 0.7654 (m100) REVERT: C 90 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 22 ARG cc_start: 0.7859 (ttt-90) cc_final: 0.7369 (mtp-110) REVERT: D 31 ASN cc_start: 0.8937 (p0) cc_final: 0.8464 (p0) REVERT: D 90 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8173 (ttp-170) REVERT: D 92 GLU cc_start: 0.8617 (mp0) cc_final: 0.7818 (mp0) REVERT: D 101 ARG cc_start: 0.7583 (tmm160) cc_final: 0.7046 (tmm-80) REVERT: D 103 ASN cc_start: 0.8369 (t0) cc_final: 0.8151 (t0) outliers start: 33 outliers final: 22 residues processed: 122 average time/residue: 0.1749 time to fit residues: 27.0107 Evaluate side-chains 114 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.0040 chunk 31 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4762 Z= 0.212 Angle : 0.603 6.402 6472 Z= 0.319 Chirality : 0.041 0.135 743 Planarity : 0.005 0.053 825 Dihedral : 6.094 76.620 728 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.92 % Allowed : 18.31 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.35), residues: 588 helix: 2.36 (0.47), residues: 129 sheet: -1.94 (0.35), residues: 187 loop : -1.34 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 554 HIS 0.003 0.001 HIS D 102 PHE 0.019 0.002 PHE A 745 TYR 0.023 0.002 TYR A 634 ARG 0.002 0.000 ARG A 826 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8786 (mp10) cc_final: 0.8446 (tp-100) REVERT: A 634 TYR cc_start: 0.8117 (t80) cc_final: 0.7562 (t80) REVERT: A 638 MET cc_start: 0.8312 (tpp) cc_final: 0.8074 (tpp) REVERT: A 688 ASP cc_start: 0.8509 (t0) cc_final: 0.7820 (m-30) REVERT: A 719 MET cc_start: 0.8240 (mmm) cc_final: 0.7758 (mpp) REVERT: A 790 PHE cc_start: 0.8363 (m-80) cc_final: 0.7398 (m-10) REVERT: B 861 MET cc_start: 0.6678 (tpp) cc_final: 0.6261 (mmm) REVERT: C 36 TRP cc_start: 0.9219 (m100) cc_final: 0.7771 (m100) REVERT: C 90 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 22 ARG cc_start: 0.7869 (ttt-90) cc_final: 0.7444 (mtp-110) REVERT: D 31 ASN cc_start: 0.8913 (p0) cc_final: 0.8448 (p0) REVERT: D 54 ILE cc_start: 0.9010 (mt) cc_final: 0.8260 (tp) REVERT: D 60 TYR cc_start: 0.8578 (t80) cc_final: 0.8346 (t80) REVERT: D 83 TYR cc_start: 0.8505 (m-80) cc_final: 0.7961 (m-80) REVERT: D 87 ASN cc_start: 0.8272 (m-40) cc_final: 0.7941 (m-40) REVERT: D 92 GLU cc_start: 0.8515 (mp0) cc_final: 0.7997 (mp0) REVERT: D 101 ARG cc_start: 0.7589 (tmm160) cc_final: 0.6358 (tmm-80) REVERT: D 103 ASN cc_start: 0.8185 (t0) cc_final: 0.7870 (t0) outliers start: 25 outliers final: 17 residues processed: 120 average time/residue: 0.1678 time to fit residues: 25.8010 Evaluate side-chains 114 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4762 Z= 0.231 Angle : 0.604 6.518 6472 Z= 0.316 Chirality : 0.041 0.153 743 Planarity : 0.004 0.051 825 Dihedral : 5.831 72.342 728 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.31 % Allowed : 20.67 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.35), residues: 588 helix: 2.85 (0.47), residues: 123 sheet: -1.67 (0.36), residues: 181 loop : -1.42 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 554 HIS 0.003 0.001 HIS D 102 PHE 0.015 0.001 PHE A 745 TYR 0.028 0.002 TYR C 56 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8769 (mp10) cc_final: 0.8419 (tp-100) REVERT: A 634 TYR cc_start: 0.8137 (t80) cc_final: 0.7595 (t80) REVERT: A 638 MET cc_start: 0.8316 (tpp) cc_final: 0.8062 (tpp) REVERT: A 688 ASP cc_start: 0.8500 (t0) cc_final: 0.7845 (m-30) REVERT: A 719 MET cc_start: 0.8369 (mmm) cc_final: 0.7854 (mpp) REVERT: A 790 PHE cc_start: 0.8376 (m-80) cc_final: 0.7389 (m-80) REVERT: A 825 LYS cc_start: 0.9182 (tptm) cc_final: 0.8947 (tptm) REVERT: B 861 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6111 (mmm) REVERT: C 36 TRP cc_start: 0.9210 (m100) cc_final: 0.7763 (m100) REVERT: C 90 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 22 ARG cc_start: 0.7809 (ttt-90) cc_final: 0.7460 (mtp-110) REVERT: D 31 ASN cc_start: 0.8944 (p0) cc_final: 0.8479 (p0) REVERT: D 41 ARG cc_start: 0.8300 (ptt180) cc_final: 0.8085 (ptt180) REVERT: D 54 ILE cc_start: 0.9024 (mt) cc_final: 0.8252 (tp) REVERT: D 60 TYR cc_start: 0.8629 (t80) cc_final: 0.8422 (t80) REVERT: D 83 TYR cc_start: 0.8453 (m-80) cc_final: 0.8007 (m-80) REVERT: D 92 GLU cc_start: 0.8485 (mp0) cc_final: 0.7922 (mp0) REVERT: D 101 ARG cc_start: 0.7663 (tmm160) cc_final: 0.6478 (tmm-80) REVERT: D 103 ASN cc_start: 0.8086 (t0) cc_final: 0.7727 (t0) outliers start: 27 outliers final: 21 residues processed: 117 average time/residue: 0.1821 time to fit residues: 26.8079 Evaluate side-chains 118 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4762 Z= 0.229 Angle : 0.619 8.201 6472 Z= 0.321 Chirality : 0.042 0.148 743 Planarity : 0.004 0.052 825 Dihedral : 5.713 70.059 728 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.91 % Allowed : 22.05 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.35), residues: 588 helix: 2.90 (0.47), residues: 123 sheet: -1.59 (0.35), residues: 188 loop : -1.44 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 554 HIS 0.003 0.001 HIS D 102 PHE 0.013 0.001 PHE A 745 TYR 0.036 0.002 TYR A 754 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8753 (mp10) cc_final: 0.8414 (tp-100) REVERT: A 634 TYR cc_start: 0.8186 (t80) cc_final: 0.7853 (t80) REVERT: A 688 ASP cc_start: 0.8463 (t0) cc_final: 0.7807 (m-30) REVERT: A 719 MET cc_start: 0.8415 (mmm) cc_final: 0.7947 (mpp) REVERT: A 790 PHE cc_start: 0.8424 (m-80) cc_final: 0.7484 (m-80) REVERT: A 825 LYS cc_start: 0.9179 (tptm) cc_final: 0.8934 (tptm) REVERT: B 861 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6069 (mmm) REVERT: C 36 TRP cc_start: 0.9211 (m100) cc_final: 0.7719 (m100) REVERT: C 90 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8081 (tm-30) REVERT: D 22 ARG cc_start: 0.7801 (ttt-90) cc_final: 0.7461 (mtp-110) REVERT: D 31 ASN cc_start: 0.8966 (p0) cc_final: 0.8500 (p0) REVERT: D 41 ARG cc_start: 0.8335 (ptt180) cc_final: 0.7424 (ptm160) REVERT: D 54 ILE cc_start: 0.9057 (mt) cc_final: 0.8313 (tp) REVERT: D 83 TYR cc_start: 0.8473 (m-80) cc_final: 0.8062 (m-80) REVERT: D 92 GLU cc_start: 0.8408 (mp0) cc_final: 0.7949 (mp0) REVERT: D 101 ARG cc_start: 0.7704 (tmm160) cc_final: 0.6545 (tmm-80) REVERT: D 103 ASN cc_start: 0.8093 (t0) cc_final: 0.7704 (t0) outliers start: 30 outliers final: 23 residues processed: 117 average time/residue: 0.1691 time to fit residues: 25.7530 Evaluate side-chains 124 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4762 Z= 0.300 Angle : 0.659 7.696 6472 Z= 0.341 Chirality : 0.043 0.147 743 Planarity : 0.005 0.052 825 Dihedral : 5.830 70.597 728 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.10 % Allowed : 21.46 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.36), residues: 588 helix: 2.76 (0.48), residues: 123 sheet: -1.75 (0.35), residues: 198 loop : -1.37 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 554 HIS 0.003 0.001 HIS A 773 PHE 0.016 0.001 PHE A 509 TYR 0.029 0.002 TYR A 754 ARG 0.003 0.000 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8781 (mp10) cc_final: 0.8395 (tp-100) REVERT: A 634 TYR cc_start: 0.8216 (t80) cc_final: 0.7968 (t80) REVERT: A 675 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 688 ASP cc_start: 0.8452 (t0) cc_final: 0.7788 (m-30) REVERT: A 719 MET cc_start: 0.8524 (mmm) cc_final: 0.8122 (mpp) REVERT: A 790 PHE cc_start: 0.8462 (m-80) cc_final: 0.7568 (m-80) REVERT: A 793 LYS cc_start: 0.9034 (tppp) cc_final: 0.8786 (tppp) REVERT: A 825 LYS cc_start: 0.9197 (tptm) cc_final: 0.8932 (tptm) REVERT: B 861 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6134 (mmm) REVERT: C 28 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8766 (tm-30) REVERT: C 36 TRP cc_start: 0.9191 (m100) cc_final: 0.7802 (m100) REVERT: C 90 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 31 ASN cc_start: 0.8977 (p0) cc_final: 0.8484 (p0) REVERT: D 41 ARG cc_start: 0.8436 (ptt180) cc_final: 0.7627 (ptm160) REVERT: D 54 ILE cc_start: 0.9100 (mt) cc_final: 0.8380 (tp) REVERT: D 92 GLU cc_start: 0.8449 (mp0) cc_final: 0.7987 (mp0) REVERT: D 101 ARG cc_start: 0.7798 (tmm160) cc_final: 0.6640 (tmm-80) REVERT: D 103 ASN cc_start: 0.8154 (t0) cc_final: 0.7756 (t0) outliers start: 31 outliers final: 25 residues processed: 118 average time/residue: 0.1706 time to fit residues: 26.1808 Evaluate side-chains 119 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.0060 chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN C 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4762 Z= 0.192 Angle : 0.615 8.480 6472 Z= 0.321 Chirality : 0.041 0.141 743 Planarity : 0.004 0.053 825 Dihedral : 5.688 71.469 728 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.12 % Allowed : 22.64 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.36), residues: 588 helix: 2.74 (0.48), residues: 123 sheet: -1.54 (0.36), residues: 188 loop : -1.48 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 554 HIS 0.003 0.000 HIS D 102 PHE 0.019 0.001 PHE A 715 TYR 0.030 0.002 TYR C 56 ARG 0.002 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8744 (mp10) cc_final: 0.8471 (tp-100) REVERT: A 675 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 688 ASP cc_start: 0.8412 (t0) cc_final: 0.7756 (m-30) REVERT: A 719 MET cc_start: 0.8495 (mmm) cc_final: 0.8114 (mpp) REVERT: A 790 PHE cc_start: 0.8448 (m-80) cc_final: 0.7551 (m-80) REVERT: A 793 LYS cc_start: 0.9003 (tppp) cc_final: 0.8779 (tppp) REVERT: A 825 LYS cc_start: 0.9175 (tptm) cc_final: 0.8940 (tptm) REVERT: B 861 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6066 (mmm) REVERT: C 90 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8006 (tm-30) REVERT: D 31 ASN cc_start: 0.8952 (p0) cc_final: 0.8477 (p0) REVERT: D 41 ARG cc_start: 0.8452 (ptt180) cc_final: 0.7658 (ptm160) REVERT: D 54 ILE cc_start: 0.9081 (mt) cc_final: 0.8371 (tp) REVERT: D 83 TYR cc_start: 0.8331 (m-80) cc_final: 0.8031 (m-80) REVERT: D 92 GLU cc_start: 0.8426 (mp0) cc_final: 0.7904 (mp0) REVERT: D 101 ARG cc_start: 0.7822 (tmm160) cc_final: 0.6668 (tmm-80) REVERT: D 103 ASN cc_start: 0.8089 (t0) cc_final: 0.7668 (t0) outliers start: 26 outliers final: 23 residues processed: 116 average time/residue: 0.1602 time to fit residues: 23.9065 Evaluate side-chains 119 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN C 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4762 Z= 0.283 Angle : 0.657 8.271 6472 Z= 0.343 Chirality : 0.043 0.143 743 Planarity : 0.005 0.051 825 Dihedral : 5.768 67.999 728 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.51 % Allowed : 22.24 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.36), residues: 588 helix: 2.47 (0.48), residues: 123 sheet: -1.78 (0.35), residues: 201 loop : -1.38 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 554 HIS 0.004 0.001 HIS D 102 PHE 0.032 0.002 PHE A 715 TYR 0.037 0.002 TYR A 634 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8759 (mp10) cc_final: 0.8412 (tp-100) REVERT: A 675 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 688 ASP cc_start: 0.8434 (t0) cc_final: 0.7783 (m-30) REVERT: A 719 MET cc_start: 0.8556 (mmm) cc_final: 0.8140 (mpp) REVERT: A 790 PHE cc_start: 0.8491 (m-80) cc_final: 0.7622 (m-80) REVERT: A 793 LYS cc_start: 0.9010 (tppp) cc_final: 0.8794 (tppp) REVERT: A 825 LYS cc_start: 0.9192 (tptm) cc_final: 0.8943 (tptm) REVERT: B 861 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6075 (mmm) REVERT: C 28 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8769 (tm-30) REVERT: C 90 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 31 ASN cc_start: 0.8951 (p0) cc_final: 0.8477 (p0) REVERT: D 41 ARG cc_start: 0.8565 (ptt180) cc_final: 0.7745 (ptm-80) REVERT: D 92 GLU cc_start: 0.8436 (mp0) cc_final: 0.7862 (mp0) REVERT: D 101 ARG cc_start: 0.7882 (tmm160) cc_final: 0.6730 (tmm-80) REVERT: D 103 ASN cc_start: 0.8200 (t0) cc_final: 0.7764 (t0) outliers start: 28 outliers final: 26 residues processed: 112 average time/residue: 0.1743 time to fit residues: 24.8592 Evaluate side-chains 119 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN C 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4762 Z= 0.225 Angle : 0.635 8.085 6472 Z= 0.329 Chirality : 0.042 0.140 743 Planarity : 0.005 0.054 825 Dihedral : 5.704 68.598 728 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.31 % Allowed : 23.23 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.35), residues: 588 helix: 2.48 (0.48), residues: 123 sheet: -1.56 (0.35), residues: 191 loop : -1.53 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 554 HIS 0.004 0.001 HIS D 102 PHE 0.031 0.002 PHE A 715 TYR 0.036 0.002 TYR A 634 ARG 0.002 0.000 ARG A 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8779 (mp10) cc_final: 0.8439 (tp-100) REVERT: A 674 GLU cc_start: 0.8189 (pt0) cc_final: 0.7931 (pt0) REVERT: A 675 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 688 ASP cc_start: 0.8416 (t0) cc_final: 0.7769 (m-30) REVERT: A 719 MET cc_start: 0.8524 (mmm) cc_final: 0.8124 (mpp) REVERT: A 790 PHE cc_start: 0.8498 (m-80) cc_final: 0.7004 (m-10) REVERT: A 793 LYS cc_start: 0.9005 (tppp) cc_final: 0.8793 (tppp) REVERT: A 825 LYS cc_start: 0.9195 (tptm) cc_final: 0.8933 (tptm) REVERT: B 861 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6070 (mmm) REVERT: C 28 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8727 (tm-30) REVERT: C 90 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8461 (tm-30) REVERT: D 31 ASN cc_start: 0.8944 (p0) cc_final: 0.8474 (p0) REVERT: D 41 ARG cc_start: 0.8589 (ptt180) cc_final: 0.7845 (ptm-80) REVERT: D 92 GLU cc_start: 0.8404 (mp0) cc_final: 0.7822 (mp0) REVERT: D 101 ARG cc_start: 0.7869 (tmm160) cc_final: 0.6746 (tmm-80) REVERT: D 103 ASN cc_start: 0.8163 (t0) cc_final: 0.7743 (t0) outliers start: 27 outliers final: 26 residues processed: 116 average time/residue: 0.1916 time to fit residues: 28.2812 Evaluate side-chains 118 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 817 ASN Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN C 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105634 restraints weight = 12257.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109704 restraints weight = 11108.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111416 restraints weight = 4544.453| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4762 Z= 0.197 Angle : 0.614 7.687 6472 Z= 0.319 Chirality : 0.043 0.177 743 Planarity : 0.004 0.053 825 Dihedral : 5.637 69.217 728 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.92 % Allowed : 24.21 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.35), residues: 588 helix: 2.44 (0.47), residues: 123 sheet: -1.52 (0.35), residues: 191 loop : -1.52 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 554 HIS 0.003 0.001 HIS D 102 PHE 0.030 0.001 PHE A 715 TYR 0.030 0.002 TYR C 56 ARG 0.002 0.000 ARG A 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.76 seconds wall clock time: 36 minutes 21.79 seconds (2181.79 seconds total)