Starting phenix.real_space_refine on Thu Jul 24 01:35:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uta_64486/07_2025/9uta_64486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uta_64486/07_2025/9uta_64486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uta_64486/07_2025/9uta_64486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uta_64486/07_2025/9uta_64486.map" model { file = "/net/cci-nas-00/data/ceres_data/9uta_64486/07_2025/9uta_64486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uta_64486/07_2025/9uta_64486.cif" } resolution = 3.77 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= 0.008 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 45 5.16 5 C 3096 2.51 5 N 764 2.21 5 O 796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4701 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2487 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "B" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2214 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 19, 'TRANS': 266} Time building chain proxies: 4.09, per 1000 atoms: 0.87 Number of scatterers: 4701 At special positions: 0 Unit cell: (71.04, 86.4, 107.52, 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 45 16.00 O 796 8.00 N 764 7.00 C 3096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 551 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 722 " distance=2.23 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 611.5 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 72.1% alpha, 4.2% 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 563 through 589 removed outlier: 3.686A pdb=" N GLY A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.654A pdb=" N ALA A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 618 removed outlier: 4.033A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.160A pdb=" N CYS A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 665 removed outlier: 3.867A pdb=" N CYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 removed outlier: 3.536A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 700 removed outlier: 4.165A pdb=" N SER A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 723 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 733 through 749 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.996A pdb=" N ALA A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 805 removed outlier: 3.921A pdb=" N ILE A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 823 through 833 removed outlier: 4.316A pdb=" N GLN A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY A 833 " --> pdb=" O SER A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 593 Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 604 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 629 through 635 Processing helix chain 'B' and resid 637 through 663 Proline residue: B 643 - end of helix removed outlier: 5.176A pdb=" N THR B 650 " --> pdb=" O GLY B 646 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 651 " --> pdb=" O CYS B 647 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.627A pdb=" N ARG B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 703 Processing helix chain 'B' and resid 727 through 749 removed outlier: 5.280A pdb=" N THR B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASN B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 784 removed outlier: 4.500A pdb=" N GLY B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 770 " --> pdb=" O PHE B 766 " (cutoff:3.500A) Proline residue: B 780 - end of helix Processing helix chain 'B' and resid 790 through 806 removed outlier: 3.985A pdb=" N GLN B 794 " --> pdb=" O ARG B 790 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET B 795 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 798 " --> pdb=" O GLN B 794 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 824 removed outlier: 4.116A pdb=" N ARG B 813 " --> pdb=" O PHE B 809 " (cutoff:3.500A) Proline residue: B 821 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557 removed outlier: 3.930A pdb=" N VAL A 718 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 558 through 560 removed outlier: 6.320A pdb=" N ARG B 558 " --> pdb=" O ALA B 718 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL B 720 " --> pdb=" O ARG B 558 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARG B 560 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N CYS B 722 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N GLU B 717 " --> pdb=" O HIS B 712 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS B 712 " --> pdb=" O GLU B 717 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 706 " --> pdb=" O ARG B 723 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 870 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: 1.19 Time building geometry restraints manager: 1.52 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: 1436 1.34 - 1.46: 1204 1.46 - 1.58: 2132 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 4834 Sorted by residual: bond pdb=" CA LEU B 806 " pdb=" C LEU B 806 " ideal model delta sigma weight residual 1.522 1.471 0.050 1.72e-02 3.38e+03 8.55e+00 bond pdb=" C PHE B 778 " pdb=" N VAL B 779 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.13e-02 7.83e+03 3.44e+00 bond pdb=" N PRO B 791 " pdb=" CA PRO B 791 " ideal model delta sigma weight residual 1.469 1.445 0.023 1.28e-02 6.10e+03 3.29e+00 bond pdb=" CB PRO B 791 " pdb=" CG PRO B 791 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.09e+00 bond pdb=" C ILE B 805 " pdb=" N LEU B 806 " ideal model delta sigma weight residual 1.333 1.307 0.026 1.56e-02 4.11e+03 2.84e+00 ... (remaining 4829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 6515 2.50 - 5.01: 84 5.01 - 7.51: 7 7.51 - 10.01: 0 10.01 - 12.51: 1 Bond angle restraints: 6607 Sorted by residual: angle pdb=" CA PRO B 791 " pdb=" N PRO B 791 " pdb=" CD PRO B 791 " ideal model delta sigma weight residual 112.00 99.49 12.51 1.40e+00 5.10e-01 7.99e+01 angle pdb=" CA PRO A 638 " pdb=" N PRO A 638 " pdb=" CD PRO A 638 " ideal model delta sigma weight residual 112.00 105.14 6.86 1.40e+00 5.10e-01 2.40e+01 angle pdb=" N VAL B 793 " pdb=" CA VAL B 793 " pdb=" C VAL B 793 " ideal model delta sigma weight residual 111.67 108.66 3.01 9.50e-01 1.11e+00 1.00e+01 angle pdb=" N PHE B 778 " pdb=" CA PHE B 778 " pdb=" CB PHE B 778 " ideal model delta sigma weight residual 110.30 114.15 -3.85 1.54e+00 4.22e-01 6.26e+00 angle pdb=" C SER B 777 " pdb=" N PHE B 778 " pdb=" CA PHE B 778 " ideal model delta sigma weight residual 120.68 116.46 4.22 1.70e+00 3.46e-01 6.17e+00 ... (remaining 6602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2464 17.98 - 35.96: 289 35.96 - 53.94: 70 53.94 - 71.91: 22 71.91 - 89.89: 3 Dihedral angle restraints: 2848 sinusoidal: 1089 harmonic: 1759 Sorted by residual: dihedral pdb=" CB CYS B 633 " pdb=" SG CYS B 633 " pdb=" SG CYS B 722 " pdb=" CB CYS B 722 " ideal model delta sinusoidal sigma weight residual 93.00 32.28 60.72 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CA ALA B 735 " pdb=" C ALA B 735 " pdb=" N THR B 736 " pdb=" CA THR B 736 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA SER A 547 " pdb=" C SER A 547 " pdb=" N GLU A 548 " pdb=" CA GLU A 548 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 466 0.029 - 0.058: 208 0.058 - 0.088: 73 0.088 - 0.117: 23 0.117 - 0.146: 8 Chirality restraints: 778 Sorted by residual: chirality pdb=" CB VAL A 786 " pdb=" CA VAL A 786 " pdb=" CG1 VAL A 786 " pdb=" CG2 VAL A 786 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA PRO B 791 " pdb=" N PRO B 791 " pdb=" C PRO B 791 " pdb=" CB PRO B 791 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE A 518 " pdb=" N ILE A 518 " pdb=" C ILE A 518 " pdb=" CB ILE A 518 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 775 not shown) Planarity restraints: 815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 790 " -0.098 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO B 791 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 791 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 791 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 637 " 0.057 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 638 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 823 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO A 824 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 824 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 824 " -0.040 5.00e-02 4.00e+02 ... (remaining 812 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 462 2.73 - 3.27: 5163 3.27 - 3.81: 7877 3.81 - 4.36: 8658 4.36 - 4.90: 14271 Nonbonded interactions: 36431 Sorted by model distance: nonbonded pdb=" O LYS A 760 " pdb=" OG1 THR A 763 " model vdw 2.186 3.040 nonbonded pdb=" O PRO A 638 " pdb=" NZ LYS A 689 " model vdw 2.210 3.120 nonbonded pdb=" O PHE A 659 " pdb=" OG SER A 663 " model vdw 2.259 3.040 nonbonded pdb=" OE1 GLU A 560 " pdb=" N TRP A 561 " model vdw 2.269 3.120 nonbonded pdb=" O PRO B 548 " pdb=" OG SER B 551 " model vdw 2.317 3.040 ... (remaining 36426 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: 59.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.420 Find NCS groups from input model: 0.060 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 : 0.006 0.197 4839 Z= 0.292 Angle : 0.831 25.899 6617 Z= 0.447 Chirality : 0.040 0.146 778 Planarity : 0.008 0.138 815 Dihedral : 16.779 89.893 1695 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.19 % Allowed : 25.05 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.33), residues: 598 helix: -0.15 (0.26), residues: 388 sheet: -1.38 (0.98), residues: 23 loop : -2.55 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 775 HIS 0.009 0.002 HIS B 734 PHE 0.023 0.002 PHE B 540 TYR 0.016 0.002 TYR A 545 ARG 0.005 0.001 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.15835 ( 292) hydrogen bonds : angle 6.17601 ( 870) SS BOND : bond 0.08805 ( 5) SS BOND : angle 10.03845 ( 10) covalent geometry : bond 0.00534 ( 4834) covalent geometry : angle 0.73416 ( 6607) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 PHE cc_start: 0.4925 (m-80) cc_final: 0.4076 (m-80) REVERT: A 733 SER cc_start: 0.8517 (p) cc_final: 0.8198 (p) REVERT: B 703 PHE cc_start: 0.6992 (m-80) cc_final: 0.6533 (t80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1813 time to fit residues: 40.1624 Evaluate side-chains 112 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN A 592 GLN A 757 ASN B 654 GLN B 734 HIS B 794 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.134806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113348 restraints weight = 11459.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116720 restraints weight = 6269.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.118988 restraints weight = 4108.922| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4839 Z= 0.173 Angle : 0.778 10.247 6617 Z= 0.386 Chirality : 0.043 0.191 778 Planarity : 0.007 0.073 815 Dihedral : 4.490 15.941 650 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.74 % Allowed : 22.35 % Favored : 70.91 % 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: -0.11 (0.34), residues: 598 helix: 0.81 (0.26), residues: 393 sheet: -0.74 (0.96), residues: 26 loop : -1.90 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 543 HIS 0.006 0.001 HIS A 528 PHE 0.011 0.001 PHE B 730 TYR 0.019 0.002 TYR B 815 ARG 0.004 0.001 ARG A 674 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 292) hydrogen bonds : angle 4.42479 ( 870) SS BOND : bond 0.00651 ( 5) SS BOND : angle 1.75971 ( 10) covalent geometry : bond 0.00383 ( 4834) covalent geometry : angle 0.77587 ( 6607) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7539 (tp30) cc_final: 0.7086 (tp30) REVERT: A 689 LYS cc_start: 0.8719 (tppt) cc_final: 0.8412 (tptp) REVERT: A 734 LEU cc_start: 0.8437 (mm) cc_final: 0.8146 (pp) REVERT: B 593 HIS cc_start: 0.7402 (m-70) cc_final: 0.6792 (m-70) REVERT: B 703 PHE cc_start: 0.7642 (m-80) cc_final: 0.6256 (t80) REVERT: B 717 GLU cc_start: 0.7580 (mp0) cc_final: 0.6979 (mp0) REVERT: B 734 HIS cc_start: 0.5500 (t-90) cc_final: 0.5166 (t-90) REVERT: B 768 MET cc_start: 0.9244 (mmp) cc_final: 0.8505 (mmp) REVERT: B 775 TRP cc_start: 0.8096 (m100) cc_final: 0.7607 (m100) REVERT: B 790 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.7922 (tpp80) outliers start: 35 outliers final: 19 residues processed: 139 average time/residue: 0.1680 time to fit residues: 29.4351 Evaluate side-chains 122 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 554 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 785 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.132230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.110175 restraints weight = 11304.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113357 restraints weight = 6312.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115533 restraints weight = 4213.046| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4839 Z= 0.159 Angle : 0.726 9.679 6617 Z= 0.358 Chirality : 0.041 0.136 778 Planarity : 0.006 0.062 815 Dihedral : 4.428 15.363 650 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 6.36 % Allowed : 23.89 % Favored : 69.75 % 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: 0.59 (0.35), residues: 598 helix: 1.39 (0.26), residues: 395 sheet: -0.60 (1.13), residues: 20 loop : -1.75 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 543 HIS 0.004 0.001 HIS A 528 PHE 0.015 0.002 PHE B 749 TYR 0.021 0.002 TYR B 815 ARG 0.003 0.001 ARG B 632 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 292) hydrogen bonds : angle 4.13383 ( 870) SS BOND : bond 0.00401 ( 5) SS BOND : angle 1.64040 ( 10) covalent geometry : bond 0.00350 ( 4834) covalent geometry : angle 0.72334 ( 6607) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7923 (tp30) cc_final: 0.7338 (tp30) REVERT: A 552 PHE cc_start: 0.5482 (m-80) cc_final: 0.5019 (m-10) REVERT: A 560 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7887 (tm-30) REVERT: A 616 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7422 (ttm) REVERT: A 633 ARG cc_start: 0.7606 (ttt180) cc_final: 0.7224 (ttt-90) REVERT: A 716 THR cc_start: 0.8151 (p) cc_final: 0.7926 (t) REVERT: A 734 LEU cc_start: 0.8503 (mm) cc_final: 0.8207 (pp) REVERT: A 739 SER cc_start: 0.9183 (t) cc_final: 0.8892 (p) REVERT: B 545 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 680 TRP cc_start: 0.6452 (m100) cc_final: 0.6223 (m-10) REVERT: B 703 PHE cc_start: 0.7553 (m-80) cc_final: 0.6006 (t80) REVERT: B 775 TRP cc_start: 0.7648 (m100) cc_final: 0.7191 (m100) REVERT: B 790 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.8027 (tpp80) outliers start: 33 outliers final: 21 residues processed: 129 average time/residue: 0.1548 time to fit residues: 25.8631 Evaluate side-chains 118 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 554 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 CYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 778 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.0270 chunk 19 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110788 restraints weight = 11232.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114184 restraints weight = 6050.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116402 restraints weight = 3922.911| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4839 Z= 0.133 Angle : 0.708 9.309 6617 Z= 0.339 Chirality : 0.039 0.119 778 Planarity : 0.006 0.054 815 Dihedral : 4.289 18.184 650 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.94 % Allowed : 25.05 % Favored : 68.02 % 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: 0.77 (0.35), residues: 598 helix: 1.46 (0.26), residues: 401 sheet: -0.08 (1.13), residues: 20 loop : -1.64 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 546 HIS 0.005 0.001 HIS A 528 PHE 0.011 0.001 PHE A 637 TYR 0.018 0.002 TYR B 815 ARG 0.005 0.000 ARG A 674 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 292) hydrogen bonds : angle 3.93168 ( 870) SS BOND : bond 0.00344 ( 5) SS BOND : angle 1.39132 ( 10) covalent geometry : bond 0.00295 ( 4834) covalent geometry : angle 0.70639 ( 6607) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.8323 (tp30) cc_final: 0.8065 (tp30) REVERT: A 616 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7419 (ttm) REVERT: A 633 ARG cc_start: 0.7556 (ttt180) cc_final: 0.7306 (ttt-90) REVERT: A 672 TRP cc_start: 0.6811 (OUTLIER) cc_final: 0.6144 (t-100) REVERT: A 739 SER cc_start: 0.9230 (t) cc_final: 0.8903 (p) REVERT: B 545 GLU cc_start: 0.8752 (mm-30) cc_final: 0.7845 (mm-30) REVERT: B 680 TRP cc_start: 0.6461 (m100) cc_final: 0.6227 (m-10) REVERT: B 695 LEU cc_start: 0.9354 (mm) cc_final: 0.9139 (pp) REVERT: B 703 PHE cc_start: 0.7791 (m-80) cc_final: 0.6224 (t80) REVERT: B 752 ARG cc_start: 0.7321 (ptm160) cc_final: 0.6977 (ptm160) REVERT: B 768 MET cc_start: 0.9263 (mmp) cc_final: 0.8563 (mmp) REVERT: B 818 MET cc_start: 0.8556 (tmm) cc_final: 0.7808 (tmm) outliers start: 36 outliers final: 24 residues processed: 128 average time/residue: 0.1440 time to fit residues: 24.2607 Evaluate side-chains 120 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 672 TRP Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 554 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 696 CYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 800 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS B 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.108050 restraints weight = 11836.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111325 restraints weight = 6451.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113460 restraints weight = 4220.568| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4839 Z= 0.160 Angle : 0.752 8.531 6617 Z= 0.366 Chirality : 0.041 0.220 778 Planarity : 0.006 0.051 815 Dihedral : 4.367 17.767 650 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 7.13 % Allowed : 26.01 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.35), residues: 598 helix: 1.45 (0.26), residues: 403 sheet: -0.30 (1.20), residues: 16 loop : -1.71 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 775 HIS 0.004 0.001 HIS A 528 PHE 0.020 0.001 PHE A 637 TYR 0.016 0.002 TYR B 815 ARG 0.003 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 292) hydrogen bonds : angle 4.10441 ( 870) SS BOND : bond 0.00289 ( 5) SS BOND : angle 1.24053 ( 10) covalent geometry : bond 0.00367 ( 4834) covalent geometry : angle 0.75061 ( 6607) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.8394 (tp30) cc_final: 0.7753 (tp30) REVERT: A 616 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7332 (ttm) REVERT: A 672 TRP cc_start: 0.6879 (OUTLIER) cc_final: 0.6577 (t-100) REVERT: A 739 SER cc_start: 0.9271 (t) cc_final: 0.9012 (p) REVERT: B 545 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 555 PHE cc_start: 0.7740 (t80) cc_final: 0.7468 (t80) REVERT: B 680 TRP cc_start: 0.6584 (m100) cc_final: 0.6327 (m-10) REVERT: B 703 PHE cc_start: 0.7850 (m-80) cc_final: 0.6171 (t80) REVERT: B 752 ARG cc_start: 0.7471 (ptm160) cc_final: 0.7100 (ptm160) REVERT: B 818 MET cc_start: 0.8653 (tmm) cc_final: 0.7984 (tmm) outliers start: 37 outliers final: 30 residues processed: 125 average time/residue: 0.1364 time to fit residues: 22.8680 Evaluate side-chains 124 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 672 TRP Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 554 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 613 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 696 CYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 800 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.131451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109882 restraints weight = 11692.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113044 restraints weight = 6425.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115194 restraints weight = 4223.601| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4839 Z= 0.133 Angle : 0.725 9.755 6617 Z= 0.349 Chirality : 0.040 0.174 778 Planarity : 0.006 0.047 815 Dihedral : 4.189 18.015 650 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 7.32 % Allowed : 25.43 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.35), residues: 598 helix: 1.59 (0.26), residues: 403 sheet: -0.31 (1.21), residues: 16 loop : -1.64 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 775 HIS 0.005 0.001 HIS A 528 PHE 0.027 0.001 PHE A 637 TYR 0.018 0.001 TYR A 724 ARG 0.004 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 292) hydrogen bonds : angle 3.94575 ( 870) SS BOND : bond 0.00256 ( 5) SS BOND : angle 1.17388 ( 10) covalent geometry : bond 0.00301 ( 4834) covalent geometry : angle 0.72457 ( 6607) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.8368 (tp30) cc_final: 0.8013 (tp30) REVERT: A 552 PHE cc_start: 0.5697 (m-10) cc_final: 0.5466 (m-10) REVERT: A 616 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7453 (ttm) REVERT: A 739 SER cc_start: 0.9330 (t) cc_final: 0.9006 (p) REVERT: B 545 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8100 (mm-30) REVERT: B 680 TRP cc_start: 0.6530 (m100) cc_final: 0.6283 (m-10) REVERT: B 717 GLU cc_start: 0.7658 (mp0) cc_final: 0.6990 (mp0) REVERT: B 752 ARG cc_start: 0.7426 (ptm160) cc_final: 0.7004 (ptm160) REVERT: B 768 MET cc_start: 0.9261 (mmp) cc_final: 0.8604 (mmp) REVERT: B 818 MET cc_start: 0.8619 (tmm) cc_final: 0.8005 (tmm) outliers start: 38 outliers final: 30 residues processed: 118 average time/residue: 0.1427 time to fit residues: 22.3874 Evaluate side-chains 120 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 554 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 613 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 696 CYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 800 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.0050 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN B 593 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.130176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108380 restraints weight = 11559.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111518 restraints weight = 6384.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.113613 restraints weight = 4247.107| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4839 Z= 0.146 Angle : 0.728 8.749 6617 Z= 0.355 Chirality : 0.041 0.166 778 Planarity : 0.006 0.045 815 Dihedral : 4.272 17.970 650 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.55 % Allowed : 27.17 % Favored : 66.28 % 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: 0.94 (0.35), residues: 598 helix: 1.64 (0.26), residues: 409 sheet: -0.37 (1.17), residues: 16 loop : -1.84 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 775 HIS 0.004 0.001 HIS A 528 PHE 0.019 0.001 PHE B 555 TYR 0.018 0.002 TYR A 724 ARG 0.006 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 292) hydrogen bonds : angle 4.01439 ( 870) SS BOND : bond 0.00243 ( 5) SS BOND : angle 1.37625 ( 10) covalent geometry : bond 0.00338 ( 4834) covalent geometry : angle 0.72707 ( 6607) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.8489 (tp30) cc_final: 0.8128 (tp30) REVERT: A 616 MET cc_start: 0.7641 (ttt) cc_final: 0.7419 (ttm) REVERT: A 739 SER cc_start: 0.9320 (t) cc_final: 0.8975 (p) REVERT: B 545 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 680 TRP cc_start: 0.6415 (m-10) cc_final: 0.5879 (m100) REVERT: B 717 GLU cc_start: 0.7625 (mp0) cc_final: 0.6991 (mp0) REVERT: B 752 ARG cc_start: 0.7449 (ptm160) cc_final: 0.7008 (ptm160) REVERT: B 768 MET cc_start: 0.9289 (mmp) cc_final: 0.8494 (mmp) REVERT: B 795 MET cc_start: 0.8383 (mmm) cc_final: 0.7997 (mmm) REVERT: B 818 MET cc_start: 0.8683 (tmm) cc_final: 0.8033 (tmm) outliers start: 34 outliers final: 29 residues processed: 115 average time/residue: 0.1391 time to fit residues: 21.1404 Evaluate side-chains 118 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 613 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 696 CYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 800 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107570 restraints weight = 11694.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.110692 restraints weight = 6364.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112811 restraints weight = 4193.538| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4839 Z= 0.146 Angle : 0.741 9.368 6617 Z= 0.363 Chirality : 0.041 0.159 778 Planarity : 0.006 0.047 815 Dihedral : 4.296 18.731 650 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.36 % Allowed : 28.13 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 598 helix: 1.69 (0.26), residues: 410 sheet: -0.50 (1.15), residues: 16 loop : -1.74 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 775 HIS 0.003 0.001 HIS A 528 PHE 0.014 0.001 PHE B 540 TYR 0.018 0.001 TYR A 724 ARG 0.006 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 292) hydrogen bonds : angle 3.94321 ( 870) SS BOND : bond 0.00751 ( 5) SS BOND : angle 0.98995 ( 10) covalent geometry : bond 0.00333 ( 4834) covalent geometry : angle 0.74105 ( 6607) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.8599 (tp30) cc_final: 0.8239 (tp30) REVERT: A 555 GLN cc_start: 0.4745 (OUTLIER) cc_final: 0.4464 (pm20) REVERT: A 739 SER cc_start: 0.9326 (t) cc_final: 0.8984 (p) REVERT: B 545 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7904 (mm-30) REVERT: B 657 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 680 TRP cc_start: 0.6488 (m-10) cc_final: 0.5916 (m100) REVERT: B 768 MET cc_start: 0.9281 (mmp) cc_final: 0.8507 (mmp) REVERT: B 795 MET cc_start: 0.8392 (mmm) cc_final: 0.8036 (mtt) REVERT: B 818 MET cc_start: 0.8704 (tmm) cc_final: 0.8098 (tmm) outliers start: 33 outliers final: 29 residues processed: 110 average time/residue: 0.1392 time to fit residues: 20.1632 Evaluate side-chains 119 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 613 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 774 THR Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 800 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.130883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.109219 restraints weight = 11434.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.112415 restraints weight = 6316.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114547 restraints weight = 4192.352| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4839 Z= 0.136 Angle : 0.737 10.104 6617 Z= 0.358 Chirality : 0.041 0.148 778 Planarity : 0.006 0.045 815 Dihedral : 4.230 17.583 650 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.39 % Allowed : 28.90 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.35), residues: 598 helix: 1.76 (0.26), residues: 409 sheet: -0.62 (1.17), residues: 16 loop : -1.87 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 775 HIS 0.003 0.001 HIS A 528 PHE 0.014 0.001 PHE B 555 TYR 0.017 0.001 TYR A 724 ARG 0.007 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 292) hydrogen bonds : angle 3.85229 ( 870) SS BOND : bond 0.00365 ( 5) SS BOND : angle 1.00184 ( 10) covalent geometry : bond 0.00305 ( 4834) covalent geometry : angle 0.73637 ( 6607) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.8589 (tp30) cc_final: 0.8212 (tp30) REVERT: A 739 SER cc_start: 0.9331 (t) cc_final: 0.8953 (p) REVERT: B 657 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 680 TRP cc_start: 0.6439 (m-10) cc_final: 0.5905 (m100) REVERT: B 768 MET cc_start: 0.9291 (mmp) cc_final: 0.8644 (mmp) REVERT: B 795 MET cc_start: 0.8412 (mmm) cc_final: 0.8007 (mtt) REVERT: B 818 MET cc_start: 0.8685 (tmm) cc_final: 0.8146 (tmm) outliers start: 28 outliers final: 25 residues processed: 105 average time/residue: 0.1422 time to fit residues: 20.4183 Evaluate side-chains 111 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 613 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 800 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.131395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109549 restraints weight = 11747.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.112628 restraints weight = 6516.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114739 restraints weight = 4356.693| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4839 Z= 0.131 Angle : 0.741 10.595 6617 Z= 0.360 Chirality : 0.040 0.147 778 Planarity : 0.006 0.044 815 Dihedral : 4.295 15.825 650 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.82 % Allowed : 29.48 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 598 helix: 1.84 (0.26), residues: 409 sheet: -0.59 (1.19), residues: 16 loop : -1.86 (0.43), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 546 HIS 0.003 0.001 HIS A 528 PHE 0.013 0.001 PHE B 778 TYR 0.024 0.002 TYR B 815 ARG 0.007 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 292) hydrogen bonds : angle 3.78718 ( 870) SS BOND : bond 0.00438 ( 5) SS BOND : angle 0.89713 ( 10) covalent geometry : bond 0.00296 ( 4834) covalent geometry : angle 0.74116 ( 6607) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.8430 (tp30) cc_final: 0.7968 (tp30) REVERT: A 555 GLN cc_start: 0.4672 (OUTLIER) cc_final: 0.4342 (pm20) REVERT: A 739 SER cc_start: 0.9314 (t) cc_final: 0.8916 (p) REVERT: A 832 GLN cc_start: 0.7768 (mt0) cc_final: 0.7161 (tm-30) REVERT: B 657 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 680 TRP cc_start: 0.6459 (m-10) cc_final: 0.5901 (m100) REVERT: B 768 MET cc_start: 0.9282 (mmp) cc_final: 0.8535 (mmp) REVERT: B 795 MET cc_start: 0.8410 (mmm) cc_final: 0.8087 (mtt) REVERT: B 818 MET cc_start: 0.8614 (tmm) cc_final: 0.8142 (tmm) outliers start: 25 outliers final: 23 residues processed: 109 average time/residue: 0.1334 time to fit residues: 19.6287 Evaluate side-chains 114 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 613 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.0270 chunk 47 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 0.0270 chunk 25 optimal weight: 0.0170 overall best weight: 0.0712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.131741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109610 restraints weight = 11628.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112733 restraints weight = 6409.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114895 restraints weight = 4281.180| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.7942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 4839 Z= 0.259 Angle : 1.230 59.200 6617 Z= 0.703 Chirality : 0.046 0.610 778 Planarity : 0.007 0.074 815 Dihedral : 4.428 27.885 650 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.82 % Allowed : 30.44 % Favored : 64.74 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 598 helix: 1.85 (0.26), residues: 409 sheet: -0.56 (1.19), residues: 16 loop : -1.88 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.188 0.005 TRP B 546 HIS 0.006 0.001 HIS A 528 PHE 0.013 0.001 PHE B 778 TYR 0.024 0.002 TYR B 815 ARG 0.036 0.001 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 292) hydrogen bonds : angle 3.88986 ( 870) SS BOND : bond 0.00424 ( 5) SS BOND : angle 0.98434 ( 10) covalent geometry : bond 0.00529 ( 4834) covalent geometry : angle 1.23043 ( 6607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.03 seconds wall clock time: 45 minutes 26.86 seconds (2726.86 seconds total)