Starting phenix.real_space_refine on Sun Jun 8 19:47:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2q_27146/06_2025/8d2q_27146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2q_27146/06_2025/8d2q_27146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2q_27146/06_2025/8d2q_27146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2q_27146/06_2025/8d2q_27146.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2q_27146/06_2025/8d2q_27146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2q_27146/06_2025/8d2q_27146.cif" } resolution = 2.58 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= 0.003 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: 6 Type Number sf(0) Gaussians P 121 5.49 5 Mg 5 5.21 5 S 17 5.16 5 C 5643 2.51 5 N 1817 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9721 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7143 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 849} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1835 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 36} Link IDs: {'rna2p': 11, 'rna3p': 74} Chain breaks: 2 Chain: "T" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "X" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.75, per 1000 atoms: 0.69 Number of scatterers: 9721 At special positions: 0 Unit cell: (96.525, 109.725, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 P 121 15.00 Mg 5 11.99 O 2118 8.00 N 1817 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 610 " distance=2.04 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 613 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 43.6% alpha, 10.7% beta 44 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.574A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 552 removed outlier: 3.848A pdb=" N ALA A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 636 through 643 Processing helix chain 'A' and resid 653 through 669 removed outlier: 3.607A pdb=" N SER A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 703 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 782 removed outlier: 4.417A pdb=" N PHE A 780 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 removed outlier: 3.707A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1024 through 1033 removed outlier: 3.992A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1071 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1094 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 711 removed outlier: 6.343A pdb=" N ILE A 513 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 710 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 515 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 24 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 44 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 26 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 42 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 28 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 824 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 590 through 591 removed outlier: 3.726A pdb=" N ASP A 590 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA4, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA5, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA6, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA7, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.641A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.527A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2206 1.33 - 1.46: 2986 1.46 - 1.58: 4720 1.58 - 1.70: 240 1.70 - 1.82: 24 Bond restraints: 10176 Sorted by residual: bond pdb=" CG PRO A 487 " pdb=" CD PRO A 487 " ideal model delta sigma weight residual 1.503 1.315 0.188 3.40e-02 8.65e+02 3.05e+01 bond pdb=" C1' DT T 23 " pdb=" N1 DT T 23 " ideal model delta sigma weight residual 1.490 1.607 -0.117 3.00e-02 1.11e+03 1.53e+01 bond pdb=" CG PRO A 476 " pdb=" CD PRO A 476 " ideal model delta sigma weight residual 1.503 1.391 0.112 3.40e-02 8.65e+02 1.09e+01 bond pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.06e+01 bond pdb=" C3' DT T 22 " pdb=" O3' DT T 22 " ideal model delta sigma weight residual 1.422 1.518 -0.096 3.00e-02 1.11e+03 1.03e+01 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 14060 2.87 - 5.75: 255 5.75 - 8.62: 38 8.62 - 11.50: 8 11.50 - 14.37: 5 Bond angle restraints: 14366 Sorted by residual: angle pdb=" CA PRO A 487 " pdb=" N PRO A 487 " pdb=" CD PRO A 487 " ideal model delta sigma weight residual 112.00 97.63 14.37 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N PRO A 487 " pdb=" CD PRO A 487 " pdb=" CG PRO A 487 " ideal model delta sigma weight residual 103.20 89.19 14.01 1.50e+00 4.44e-01 8.73e+01 angle pdb=" C3' A B 12 " pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 120.20 133.24 -13.04 1.50e+00 4.44e-01 7.56e+01 angle pdb=" C PRO A 675 " pdb=" N GLU A 676 " pdb=" CA GLU A 676 " ideal model delta sigma weight residual 121.70 134.99 -13.29 1.80e+00 3.09e-01 5.45e+01 angle pdb=" N GLU A1067 " pdb=" CA GLU A1067 " pdb=" CB GLU A1067 " ideal model delta sigma weight residual 110.12 120.81 -10.69 1.47e+00 4.63e-01 5.28e+01 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 5612 31.09 - 62.17: 457 62.17 - 93.26: 103 93.26 - 124.34: 3 124.34 - 155.43: 4 Dihedral angle restraints: 6179 sinusoidal: 3563 harmonic: 2616 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -5.03 -80.97 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A 578 " pdb=" SG CYS A 578 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -166.52 80.52 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -162.59 76.59 1 1.00e+01 1.00e-02 7.37e+01 ... (remaining 6176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1450 0.076 - 0.151: 177 0.151 - 0.227: 19 0.227 - 0.303: 5 0.303 - 0.378: 2 Chirality restraints: 1653 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA GLU A1067 " pdb=" N GLU A1067 " pdb=" C GLU A1067 " pdb=" CB GLU A1067 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1' A B 12 " pdb=" O4' A B 12 " pdb=" C2' A B 12 " pdb=" N9 A B 12 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1650 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 486 " 0.082 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 487 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 22 " 0.032 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" N1 DT T 22 " -0.068 2.00e-02 2.50e+03 pdb=" C2 DT T 22 " 0.025 2.00e-02 2.50e+03 pdb=" O2 DT T 22 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DT T 22 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT T 22 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT T 22 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1063 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C VAL A1063 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL A1063 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A1064 " 0.018 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 281 2.67 - 3.23: 8105 3.23 - 3.79: 18047 3.79 - 4.34: 23052 4.34 - 4.90: 34466 Nonbonded interactions: 83951 Sorted by model distance: nonbonded pdb=" OD2 ASP A 18 " pdb="MG MG A1201 " model vdw 2.113 2.170 nonbonded pdb=" ND1 HIS A 750 " pdb="MG MG A1201 " model vdw 2.158 2.250 nonbonded pdb=" OP1 C B 52 " pdb="MG MG B 204 " model vdw 2.241 2.170 nonbonded pdb=" OG SER A 59 " pdb=" OP1 C B 17 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR A 684 " pdb=" OP1 DT T 23 " model vdw 2.256 3.040 ... (remaining 83946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.080 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:17.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 0.188 10181 Z= 0.272 Angle : 0.976 14.373 14376 Z= 0.526 Chirality : 0.052 0.378 1653 Planarity : 0.009 0.115 1420 Dihedral : 20.817 155.427 4468 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.68 (0.25), residues: 898 helix: -1.09 (0.23), residues: 397 sheet: -0.27 (0.54), residues: 85 loop : -1.19 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 942 HIS 0.007 0.002 HIS A 574 PHE 0.047 0.003 PHE A 76 TYR 0.023 0.002 TYR A 698 ARG 0.021 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.08606 ( 432) hydrogen bonds : angle 5.78117 ( 1150) SS BOND : bond 0.00400 ( 5) SS BOND : angle 2.36256 ( 10) covalent geometry : bond 0.00593 (10176) covalent geometry : angle 0.97432 (14366) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.875 Fit side-chains REVERT: A 487 PRO cc_start: 0.6995 (Cg_exo) cc_final: 0.6628 (Cg_endo) REVERT: A 804 LYS cc_start: 0.8030 (tttp) cc_final: 0.7803 (tppt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.8892 time to fit residues: 143.4666 Evaluate side-chains 57 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 802 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.206119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157660 restraints weight = 9517.377| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.73 r_work: 0.3406 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10181 Z= 0.154 Angle : 0.613 7.751 14376 Z= 0.319 Chirality : 0.039 0.308 1653 Planarity : 0.005 0.043 1420 Dihedral : 22.203 155.130 2766 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.94 % Allowed : 5.26 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: -0.38 (0.26), residues: 898 helix: 0.46 (0.25), residues: 395 sheet: -0.33 (0.53), residues: 84 loop : -0.87 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.005 0.001 HIS A 749 PHE 0.025 0.002 PHE A 76 TYR 0.011 0.001 TYR A 986 ARG 0.008 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05814 ( 432) hydrogen bonds : angle 4.41086 ( 1150) SS BOND : bond 0.00232 ( 5) SS BOND : angle 1.72568 ( 10) covalent geometry : bond 0.00326 (10176) covalent geometry : angle 0.61162 (14366) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.842 Fit side-chains REVERT: A 576 MET cc_start: 0.1884 (OUTLIER) cc_final: 0.1491 (mmt) REVERT: A 804 LYS cc_start: 0.8110 (tttp) cc_final: 0.7880 (tppt) REVERT: A 805 GLU cc_start: 0.7515 (tp30) cc_final: 0.6886 (tp30) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 1.6852 time to fit residues: 118.3837 Evaluate side-chains 62 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 802 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156500 restraints weight = 9529.635| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.74 r_work: 0.3362 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10181 Z= 0.172 Angle : 0.609 8.257 14376 Z= 0.317 Chirality : 0.040 0.303 1653 Planarity : 0.005 0.040 1420 Dihedral : 22.158 162.407 2766 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.21 % Allowed : 6.87 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.13 (0.27), residues: 898 helix: 1.06 (0.26), residues: 397 sheet: -0.37 (0.53), residues: 84 loop : -0.73 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.004 0.001 HIS A 486 PHE 0.027 0.002 PHE A 76 TYR 0.017 0.002 TYR A 698 ARG 0.008 0.001 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 432) hydrogen bonds : angle 4.06712 ( 1150) SS BOND : bond 0.00330 ( 5) SS BOND : angle 1.52846 ( 10) covalent geometry : bond 0.00365 (10176) covalent geometry : angle 0.60752 (14366) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8239 (mt0) cc_final: 0.7788 (mt0) REVERT: A 804 LYS cc_start: 0.8119 (tttp) cc_final: 0.7900 (tppt) REVERT: A 805 GLU cc_start: 0.7247 (tp30) cc_final: 0.6626 (tp30) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 1.4924 time to fit residues: 106.7222 Evaluate side-chains 62 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 42 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 802 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.205876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158333 restraints weight = 9541.537| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.71 r_work: 0.3394 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10181 Z= 0.135 Angle : 0.554 7.704 14376 Z= 0.291 Chirality : 0.038 0.287 1653 Planarity : 0.004 0.055 1420 Dihedral : 22.073 163.893 2766 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.08 % Allowed : 8.76 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.42 (0.27), residues: 898 helix: 1.39 (0.26), residues: 396 sheet: -0.35 (0.54), residues: 84 loop : -0.64 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 486 PHE 0.025 0.001 PHE A 76 TYR 0.016 0.001 TYR A 698 ARG 0.009 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05336 ( 432) hydrogen bonds : angle 3.88234 ( 1150) SS BOND : bond 0.00180 ( 5) SS BOND : angle 1.58787 ( 10) covalent geometry : bond 0.00284 (10176) covalent geometry : angle 0.55257 (14366) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8190 (mt0) cc_final: 0.7780 (mt0) REVERT: A 802 GLN cc_start: 0.6985 (tp40) cc_final: 0.6470 (tt0) REVERT: A 805 GLU cc_start: 0.7234 (tp30) cc_final: 0.6617 (tp30) REVERT: A 895 GLU cc_start: 0.6555 (mp0) cc_final: 0.6073 (pm20) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 1.4181 time to fit residues: 98.4629 Evaluate side-chains 59 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 48 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.203045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153641 restraints weight = 9416.744| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.73 r_work: 0.3350 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10181 Z= 0.198 Angle : 0.627 7.316 14376 Z= 0.324 Chirality : 0.041 0.300 1653 Planarity : 0.005 0.055 1420 Dihedral : 22.084 164.023 2766 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.89 % Allowed : 9.84 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.32 (0.27), residues: 898 helix: 1.26 (0.26), residues: 398 sheet: -0.43 (0.55), residues: 84 loop : -0.63 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 145 HIS 0.004 0.001 HIS A 486 PHE 0.028 0.002 PHE A 76 TYR 0.019 0.002 TYR A 698 ARG 0.011 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.06156 ( 432) hydrogen bonds : angle 3.98599 ( 1150) SS BOND : bond 0.00337 ( 5) SS BOND : angle 1.70777 ( 10) covalent geometry : bond 0.00422 (10176) covalent geometry : angle 0.62521 (14366) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8330 (mt0) cc_final: 0.7911 (mt0) REVERT: A 805 GLU cc_start: 0.7482 (tp30) cc_final: 0.6842 (tp30) REVERT: A 894 ASP cc_start: 0.6845 (t0) cc_final: 0.6373 (t0) REVERT: A 895 GLU cc_start: 0.6765 (mp0) cc_final: 0.6050 (pm20) outliers start: 14 outliers final: 7 residues processed: 68 average time/residue: 1.4870 time to fit residues: 107.9694 Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 802 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.204177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154974 restraints weight = 9507.008| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.69 r_work: 0.3372 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10181 Z= 0.159 Angle : 0.579 7.049 14376 Z= 0.302 Chirality : 0.039 0.288 1653 Planarity : 0.004 0.039 1420 Dihedral : 21.981 164.276 2766 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.75 % Allowed : 11.05 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.49 (0.27), residues: 898 helix: 1.38 (0.26), residues: 398 sheet: -0.29 (0.58), residues: 79 loop : -0.54 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.005 0.001 HIS A 486 PHE 0.028 0.002 PHE A 76 TYR 0.020 0.001 TYR A 698 ARG 0.005 0.000 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.05693 ( 432) hydrogen bonds : angle 3.89656 ( 1150) SS BOND : bond 0.00245 ( 5) SS BOND : angle 1.69396 ( 10) covalent geometry : bond 0.00338 (10176) covalent geometry : angle 0.57771 (14366) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8302 (mt0) cc_final: 0.7875 (mt0) REVERT: A 802 GLN cc_start: 0.7060 (tp-100) cc_final: 0.6671 (tt0) REVERT: A 805 GLU cc_start: 0.7422 (tp30) cc_final: 0.6793 (tp30) REVERT: A 894 ASP cc_start: 0.6819 (t0) cc_final: 0.6395 (t0) REVERT: A 895 GLU cc_start: 0.6670 (mp0) cc_final: 0.6032 (pm20) outliers start: 13 outliers final: 6 residues processed: 68 average time/residue: 1.5002 time to fit residues: 109.1975 Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.0980 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 76 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.206289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161424 restraints weight = 9636.233| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.80 r_work: 0.3379 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10181 Z= 0.123 Angle : 0.533 6.445 14376 Z= 0.280 Chirality : 0.037 0.273 1653 Planarity : 0.004 0.037 1420 Dihedral : 21.830 165.081 2766 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.21 % Allowed : 11.86 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.70 (0.28), residues: 898 helix: 1.60 (0.27), residues: 397 sheet: -0.16 (0.59), residues: 79 loop : -0.47 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 PHE 0.025 0.001 PHE A 76 TYR 0.018 0.001 TYR A 187 ARG 0.013 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 432) hydrogen bonds : angle 3.75179 ( 1150) SS BOND : bond 0.00179 ( 5) SS BOND : angle 1.65435 ( 10) covalent geometry : bond 0.00258 (10176) covalent geometry : angle 0.53100 (14366) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8137 (mt0) cc_final: 0.7729 (mt0) REVERT: A 802 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6617 (tt0) REVERT: A 805 GLU cc_start: 0.7252 (tp30) cc_final: 0.6623 (tp30) REVERT: A 894 ASP cc_start: 0.6724 (t0) cc_final: 0.6440 (t0) REVERT: A 895 GLU cc_start: 0.6533 (mp0) cc_final: 0.5915 (pm20) outliers start: 9 outliers final: 4 residues processed: 68 average time/residue: 1.5666 time to fit residues: 113.5825 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 0.9980 chunk 28 optimal weight: 0.0060 chunk 4 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.206842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159258 restraints weight = 9676.437| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.89 r_work: 0.3387 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10181 Z= 0.120 Angle : 0.540 10.645 14376 Z= 0.282 Chirality : 0.037 0.267 1653 Planarity : 0.004 0.039 1420 Dihedral : 21.700 165.816 2766 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.08 % Allowed : 12.40 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.79 (0.28), residues: 898 helix: 1.72 (0.27), residues: 395 sheet: -0.10 (0.59), residues: 79 loop : -0.47 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 PHE 0.022 0.001 PHE A 76 TYR 0.014 0.001 TYR A 698 ARG 0.009 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 432) hydrogen bonds : angle 3.68220 ( 1150) SS BOND : bond 0.00173 ( 5) SS BOND : angle 1.65776 ( 10) covalent geometry : bond 0.00252 (10176) covalent geometry : angle 0.53816 (14366) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8142 (mt0) cc_final: 0.7850 (mt0) REVERT: A 802 GLN cc_start: 0.6967 (tp-100) cc_final: 0.6662 (tt0) REVERT: A 805 GLU cc_start: 0.7209 (tp30) cc_final: 0.6609 (tp30) REVERT: A 895 GLU cc_start: 0.6416 (mp0) cc_final: 0.5865 (pm20) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 1.9270 time to fit residues: 131.6218 Evaluate side-chains 60 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS A1060 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.202302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154088 restraints weight = 9539.117| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.82 r_work: 0.3319 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10181 Z= 0.239 Angle : 0.670 9.033 14376 Z= 0.344 Chirality : 0.042 0.302 1653 Planarity : 0.006 0.062 1420 Dihedral : 21.839 164.375 2766 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.21 % Allowed : 12.53 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.45 (0.28), residues: 898 helix: 1.37 (0.26), residues: 398 sheet: -0.33 (0.59), residues: 79 loop : -0.59 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 145 HIS 0.005 0.001 HIS A 486 PHE 0.031 0.002 PHE A 76 TYR 0.023 0.002 TYR A 698 ARG 0.015 0.001 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.06372 ( 432) hydrogen bonds : angle 3.99050 ( 1150) SS BOND : bond 0.00356 ( 5) SS BOND : angle 1.82140 ( 10) covalent geometry : bond 0.00516 (10176) covalent geometry : angle 0.66853 (14366) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8276 (mt0) cc_final: 0.7842 (mt0) REVERT: A 802 GLN cc_start: 0.6998 (tp-100) cc_final: 0.6658 (tt0) REVERT: A 805 GLU cc_start: 0.7281 (tp30) cc_final: 0.6644 (tp30) REVERT: A 895 GLU cc_start: 0.6672 (mp0) cc_final: 0.5951 (pm20) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 1.8865 time to fit residues: 120.5781 Evaluate side-chains 60 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.201074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148792 restraints weight = 9526.515| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.00 r_work: 0.3305 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10181 Z= 0.236 Angle : 0.674 8.455 14376 Z= 0.347 Chirality : 0.043 0.302 1653 Planarity : 0.006 0.048 1420 Dihedral : 21.906 163.138 2766 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.21 % Allowed : 12.94 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.28 (0.27), residues: 898 helix: 1.22 (0.26), residues: 398 sheet: -0.40 (0.59), residues: 79 loop : -0.67 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 145 HIS 0.005 0.001 HIS A 486 PHE 0.032 0.002 PHE A 76 TYR 0.027 0.002 TYR A 698 ARG 0.017 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.06276 ( 432) hydrogen bonds : angle 4.03245 ( 1150) SS BOND : bond 0.00373 ( 5) SS BOND : angle 1.89216 ( 10) covalent geometry : bond 0.00508 (10176) covalent geometry : angle 0.67225 (14366) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8331 (mt0) cc_final: 0.7860 (mt0) REVERT: A 802 GLN cc_start: 0.6955 (tp-100) cc_final: 0.6564 (tt0) REVERT: A 805 GLU cc_start: 0.7318 (tp30) cc_final: 0.6652 (tp30) REVERT: A 895 GLU cc_start: 0.6860 (mp0) cc_final: 0.6017 (pm20) REVERT: A 1077 GLU cc_start: 0.6753 (tp30) cc_final: 0.6521 (tp30) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 1.8612 time to fit residues: 120.0598 Evaluate side-chains 59 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 94 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.204064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157140 restraints weight = 9526.237| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.82 r_work: 0.3349 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10181 Z= 0.158 Angle : 0.595 8.111 14376 Z= 0.310 Chirality : 0.039 0.282 1653 Planarity : 0.005 0.100 1420 Dihedral : 21.803 163.739 2766 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.81 % Allowed : 13.21 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.48 (0.28), residues: 898 helix: 1.43 (0.26), residues: 397 sheet: -0.34 (0.61), residues: 79 loop : -0.59 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.005 0.001 HIS A 486 PHE 0.030 0.002 PHE A 76 TYR 0.024 0.001 TYR A 698 ARG 0.010 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 432) hydrogen bonds : angle 3.88446 ( 1150) SS BOND : bond 0.00239 ( 5) SS BOND : angle 1.77293 ( 10) covalent geometry : bond 0.00335 (10176) covalent geometry : angle 0.59320 (14366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7365.98 seconds wall clock time: 129 minutes 23.57 seconds (7763.57 seconds total)