Starting phenix.real_space_refine on Thu Jul 2 19:19:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_27146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_27146.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_27146.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_27146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_27146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_27146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2q_27146/07_2026/8d2q_27146.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, '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: 2.64, per 1000 atoms: 0.27 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: 0.75 Conformation dependent library (CDL) restraints added in 212.7 milliseconds 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: 0.97 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: 1.78 Time building geometry restraints manager: 0.99 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=" C1' DT T 23 " pdb=" N1 DT T 23 " ideal model delta sigma weight residual 1.468 1.607 -0.139 1.40e-02 5.10e+03 9.90e+01 bond pdb=" C3' DT T 22 " pdb=" O3' DT T 22 " ideal model delta sigma weight residual 1.435 1.518 -0.083 1.30e-02 5.92e+03 4.09e+01 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=" C3' DC T 21 " pdb=" O3' DC T 21 " ideal model delta sigma weight residual 1.435 1.371 0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" C3' DC D 35 " pdb=" O3' DC D 35 " ideal model delta sigma weight residual 1.435 1.493 -0.058 1.30e-02 5.92e+03 2.01e+01 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 14046 2.87 - 5.75: 270 5.75 - 8.62: 37 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=" O4' DT T 22 " pdb=" C1' DT T 22 " pdb=" N1 DT T 22 " ideal model delta sigma weight residual 108.00 113.39 -5.39 7.00e-01 2.04e+00 5.93e+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 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 5577 31.09 - 62.17: 424 62.17 - 93.26: 103 93.26 - 124.34: 3 124.34 - 155.43: 4 Dihedral angle restraints: 6111 sinusoidal: 3495 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 6108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1440 0.076 - 0.151: 187 0.151 - 0.227: 18 0.227 - 0.303: 6 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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= 0.384 Angle : 0.995 14.373 14376 Z= 0.590 Chirality : 0.054 0.378 1653 Planarity : 0.009 0.115 1420 Dihedral : 20.479 155.427 4400 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.021 0.001 ARG A1048 TYR 0.023 0.002 TYR A 698 PHE 0.047 0.003 PHE A 76 TRP 0.012 0.002 TRP A 942 HIS 0.007 0.002 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.38 (10176) covalent geometry : angle 0.99320 / 0.59 (14366) SS BOND : bond 0.00400 / 0.23 ( 5) SS BOND : angle 2.36256 / 1.38 ( 10) hydrogen bonds : bond 0.08606 / 7.08 ( 432) hydrogen bonds : angle 5.78117 / 4.01 ( 1150) *********************** 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 : 0.231 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: 0.6728 time to fit residues: 50.9872 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 : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4344 r_free = 0.4344 target = 0.207154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157766 restraints weight = 9568.983| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.71 r_work: 0.3428 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10181 Z= 0.146 Angle : 0.622 7.484 14376 Z= 0.332 Chirality : 0.040 0.298 1653 Planarity : 0.005 0.044 1420 Dihedral : 21.843 157.841 2698 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 5.39 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 898 helix: 0.37 (0.25), residues: 395 sheet: -0.14 (0.54), residues: 83 loop : -0.93 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1048 TYR 0.012 0.001 TYR A 698 PHE 0.026 0.001 PHE A 76 TRP 0.008 0.001 TRP A 942 HIS 0.005 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (10176) covalent geometry : angle 0.62045 / 0.33 (14366) SS BOND : bond 0.00241 / 0.16 ( 5) SS BOND : angle 1.66317 / 0.98 ( 10) hydrogen bonds : bond 0.06030 / 4.25 ( 432) hydrogen bonds : angle 4.53169 / 3.19 ( 1150) *********************** 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 67 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.257 Fit side-chains REVERT: A 576 MET cc_start: 0.1807 (OUTLIER) cc_final: 0.1418 (mmt) REVERT: A 802 GLN cc_start: 0.7074 (tp40) cc_final: 0.6484 (tt0) REVERT: A 804 LYS cc_start: 0.8085 (tttp) cc_final: 0.7844 (tppt) outliers start: 5 outliers final: 0 residues processed: 64 average time/residue: 0.5360 time to fit residues: 36.6870 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 10 optimal weight: 9.9990 overall best weight: 3.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.202305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153728 restraints weight = 9466.656| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.84 r_work: 0.3313 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10181 Z= 0.263 Angle : 0.740 8.766 14376 Z= 0.382 Chirality : 0.047 0.335 1653 Planarity : 0.007 0.048 1420 Dihedral : 21.895 159.727 2698 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.48 % Allowed : 6.47 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 898 helix: 0.75 (0.26), residues: 396 sheet: -0.42 (0.53), residues: 84 loop : -0.86 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1107 TYR 0.023 0.002 TYR A 698 PHE 0.030 0.003 PHE A 76 TRP 0.014 0.002 TRP A 145 HIS 0.004 0.002 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.26 (10176) covalent geometry : angle 0.73942 / 0.38 (14366) SS BOND : bond 0.00329 / 0.23 ( 5) SS BOND : angle 1.54893 / 0.98 ( 10) hydrogen bonds : bond 0.07017 / 4.92 ( 432) hydrogen bonds : angle 4.38801 / 3.09 ( 1150) *********************** 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: 11 poor density : 60 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8268 (mt0) cc_final: 0.7863 (mt0) REVERT: A 576 MET cc_start: 0.2031 (OUTLIER) cc_final: 0.1763 (mmt) REVERT: A 804 LYS cc_start: 0.8103 (tttp) cc_final: 0.7882 (tppt) REVERT: A 805 GLU cc_start: 0.7255 (tp30) cc_final: 0.6631 (tp30) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.5726 time to fit residues: 40.7471 Evaluate side-chains 62 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 576 MET Chi-restraints excluded: chain A residue 849 THR 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 87 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4306 r_free = 0.4306 target = 0.203230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154341 restraints weight = 9588.189| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.79 r_work: 0.3339 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10181 Z= 0.194 Angle : 0.645 8.097 14376 Z= 0.339 Chirality : 0.043 0.313 1653 Planarity : 0.005 0.047 1420 Dihedral : 21.893 160.130 2698 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.75 % Allowed : 9.30 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 898 helix: 0.96 (0.26), residues: 397 sheet: -0.32 (0.56), residues: 79 loop : -0.68 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.016 0.002 TYR A 986 PHE 0.030 0.002 PHE A 76 TRP 0.008 0.001 TRP A 721 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (10176) covalent geometry : angle 0.64427 / 0.34 (14366) SS BOND : bond 0.00264 / 0.17 ( 5) SS BOND : angle 1.59040 / 1.00 ( 10) hydrogen bonds : bond 0.06261 / 4.35 ( 432) hydrogen bonds : angle 4.18149 / 2.95 ( 1150) *********************** 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 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8247 (mt0) cc_final: 0.7802 (mt0) REVERT: A 191 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6739 (ttm170) REVERT: A 689 VAL cc_start: 0.7865 (t) cc_final: 0.7588 (t) REVERT: A 804 LYS cc_start: 0.8098 (tttp) cc_final: 0.7869 (tppt) REVERT: A 805 GLU cc_start: 0.7284 (tp30) cc_final: 0.6648 (tp30) outliers start: 13 outliers final: 6 residues processed: 66 average time/residue: 0.7572 time to fit residues: 53.0287 Evaluate side-chains 62 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 191 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4312 r_free = 0.4312 target = 0.203931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153675 restraints weight = 9569.537| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.83 r_work: 0.3362 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10181 Z= 0.166 Angle : 0.616 9.372 14376 Z= 0.325 Chirality : 0.042 0.305 1653 Planarity : 0.005 0.053 1420 Dihedral : 21.852 161.201 2698 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.62 % Allowed : 10.24 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 898 helix: 1.15 (0.26), residues: 398 sheet: -0.35 (0.58), residues: 79 loop : -0.61 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.021 0.002 TYR A 698 PHE 0.029 0.002 PHE A 76 TRP 0.008 0.001 TRP A 145 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (10176) covalent geometry : angle 0.61448 / 0.32 (14366) SS BOND : bond 0.00262 / 0.17 ( 5) SS BOND : angle 1.65065 / 1.03 ( 10) hydrogen bonds : bond 0.06013 / 4.15 ( 432) hydrogen bonds : angle 4.04711 / 2.85 ( 1150) *********************** 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: 12 poor density : 61 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8314 (mt0) cc_final: 0.7906 (mt0) REVERT: A 191 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6790 (ttm170) REVERT: A 576 MET cc_start: 0.1925 (OUTLIER) cc_final: 0.1682 (mmt) REVERT: A 689 VAL cc_start: 0.7896 (t) cc_final: 0.7565 (t) REVERT: A 804 LYS cc_start: 0.8186 (tttp) cc_final: 0.7962 (tppt) REVERT: A 805 GLU cc_start: 0.7445 (tp30) cc_final: 0.6814 (tp30) REVERT: A 895 GLU cc_start: 0.6715 (mp0) cc_final: 0.6044 (pm20) outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.7086 time to fit residues: 50.6090 Evaluate side-chains 65 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 576 MET 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 79 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4311 r_free = 0.4311 target = 0.203744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155820 restraints weight = 9577.729| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.80 r_work: 0.3348 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10181 Z= 0.167 Angle : 0.607 7.841 14376 Z= 0.321 Chirality : 0.041 0.301 1653 Planarity : 0.005 0.046 1420 Dihedral : 21.830 162.571 2698 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.75 % Allowed : 11.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.27), residues: 898 helix: 1.24 (0.26), residues: 398 sheet: -0.36 (0.59), residues: 79 loop : -0.60 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1048 TYR 0.023 0.002 TYR A 698 PHE 0.030 0.002 PHE A 76 TRP 0.010 0.001 TRP A 145 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (10176) covalent geometry : angle 0.60533 / 0.32 (14366) SS BOND : bond 0.00257 / 0.16 ( 5) SS BOND : angle 1.68148 / 1.05 ( 10) hydrogen bonds : bond 0.05958 / 4.10 ( 432) hydrogen bonds : angle 3.99508 / 2.81 ( 1150) *********************** 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 75 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8235 (mt0) cc_final: 0.7816 (mt0) REVERT: A 191 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6774 (ttm170) REVERT: A 804 LYS cc_start: 0.8123 (tttp) cc_final: 0.7904 (tppt) REVERT: A 805 GLU cc_start: 0.7252 (tp30) cc_final: 0.6631 (tp30) REVERT: A 895 GLU cc_start: 0.6645 (mp0) cc_final: 0.6101 (pm20) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 0.7372 time to fit residues: 53.2969 Evaluate side-chains 66 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 191 ARG 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 Chi-restraints excluded: chain A residue 1007 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4302 r_free = 0.4302 target = 0.202897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153824 restraints weight = 9478.360| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.83 r_work: 0.3338 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10181 Z= 0.195 Angle : 0.644 8.517 14376 Z= 0.338 Chirality : 0.043 0.305 1653 Planarity : 0.005 0.049 1420 Dihedral : 21.819 162.867 2698 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.02 % Allowed : 11.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 898 helix: 1.20 (0.26), residues: 398 sheet: -0.40 (0.59), residues: 79 loop : -0.64 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1048 TYR 0.027 0.002 TYR A 698 PHE 0.031 0.002 PHE A 76 TRP 0.010 0.001 TRP A 145 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (10176) covalent geometry : angle 0.64256 / 0.34 (14366) SS BOND : bond 0.00288 / 0.19 ( 5) SS BOND : angle 1.75609 / 1.10 ( 10) hydrogen bonds : bond 0.06250 / 4.29 ( 432) hydrogen bonds : angle 4.05471 / 2.86 ( 1150) *********************** 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 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8242 (mt0) cc_final: 0.7811 (mt0) REVERT: A 191 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6737 (ttm170) REVERT: A 804 LYS cc_start: 0.8169 (tttp) cc_final: 0.7953 (tppt) REVERT: A 805 GLU cc_start: 0.7207 (tp30) cc_final: 0.6603 (tp30) REVERT: A 894 ASP cc_start: 0.6652 (t0) cc_final: 0.6285 (t0) REVERT: A 895 GLU cc_start: 0.6556 (mp0) cc_final: 0.6043 (pm20) outliers start: 15 outliers final: 8 residues processed: 66 average time/residue: 0.7595 time to fit residues: 53.2314 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 : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 191 ARG 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 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1007 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4290 r_free = 0.4290 target = 0.201662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151811 restraints weight = 9482.811| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.84 r_work: 0.3320 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10181 Z= 0.250 Angle : 0.711 8.253 14376 Z= 0.369 Chirality : 0.046 0.317 1653 Planarity : 0.006 0.060 1420 Dihedral : 21.852 162.412 2698 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.16 % Allowed : 11.46 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.27), residues: 898 helix: 1.03 (0.26), residues: 398 sheet: -0.46 (0.58), residues: 79 loop : -0.72 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.030 0.002 TYR A 698 PHE 0.033 0.002 PHE A 76 TRP 0.014 0.002 TRP A 145 HIS 0.005 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.25 (10176) covalent geometry : angle 0.70910 / 0.37 (14366) SS BOND : bond 0.00357 / 0.24 ( 5) SS BOND : angle 1.86908 / 1.18 ( 10) hydrogen bonds : bond 0.06779 / 4.66 ( 432) hydrogen bonds : angle 4.16788 / 2.94 ( 1150) *********************** 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 75 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8347 (mt0) cc_final: 0.7917 (mt0) REVERT: A 191 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6899 (ttm170) REVERT: A 804 LYS cc_start: 0.8202 (tttp) cc_final: 0.7977 (tppt) REVERT: A 805 GLU cc_start: 0.7500 (tp30) cc_final: 0.6884 (tp30) REVERT: A 894 ASP cc_start: 0.6840 (t0) cc_final: 0.6402 (t0) REVERT: A 895 GLU cc_start: 0.6788 (mp0) cc_final: 0.6081 (pm20) outliers start: 16 outliers final: 11 residues processed: 69 average time/residue: 0.7624 time to fit residues: 55.8644 Evaluate side-chains 66 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1007 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 0.0570 chunk 75 optimal weight: 0.9980 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4314 r_free = 0.4314 target = 0.204374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152649 restraints weight = 9517.348| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.70 r_work: 0.3378 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10181 Z= 0.146 Angle : 0.594 7.821 14376 Z= 0.316 Chirality : 0.041 0.294 1653 Planarity : 0.004 0.044 1420 Dihedral : 21.775 163.488 2698 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.94 % Allowed : 13.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.27), residues: 898 helix: 1.29 (0.26), residues: 398 sheet: -0.37 (0.60), residues: 79 loop : -0.59 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1048 TYR 0.021 0.001 TYR A 698 PHE 0.028 0.002 PHE A 76 TRP 0.009 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (10176) covalent geometry : angle 0.59200 / 0.31 (14366) SS BOND : bond 0.00243 / 0.15 ( 5) SS BOND : angle 1.77872 / 1.10 ( 10) hydrogen bonds : bond 0.05804 / 3.95 ( 432) hydrogen bonds : angle 3.96532 / 2.81 ( 1150) *********************** 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 65 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8289 (mt0) cc_final: 0.7866 (mt0) REVERT: A 191 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6879 (ttm170) REVERT: A 802 GLN cc_start: 0.7236 (tp40) cc_final: 0.6600 (tt0) REVERT: A 804 LYS cc_start: 0.8122 (tttp) cc_final: 0.7908 (tppt) REVERT: A 805 GLU cc_start: 0.7373 (tp30) cc_final: 0.6760 (tp30) REVERT: A 882 LEU cc_start: 0.8317 (tp) cc_final: 0.8022 (tp) REVERT: A 894 ASP cc_start: 0.6850 (t0) cc_final: 0.6385 (t0) REVERT: A 895 GLU cc_start: 0.6753 (mp0) cc_final: 0.5977 (pm20) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.7580 time to fit residues: 50.7707 Evaluate side-chains 62 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 764 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4292 r_free = 0.4292 target = 0.202117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151350 restraints weight = 9350.860| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.70 r_work: 0.3331 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10181 Z= 0.220 Angle : 0.669 8.015 14376 Z= 0.349 Chirality : 0.044 0.307 1653 Planarity : 0.005 0.050 1420 Dihedral : 21.751 162.373 2698 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.48 % Allowed : 12.40 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.27), residues: 898 helix: 1.25 (0.26), residues: 398 sheet: -0.45 (0.59), residues: 79 loop : -0.63 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1048 TYR 0.030 0.002 TYR A 698 PHE 0.032 0.002 PHE A 76 TRP 0.012 0.002 TRP A 145 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (10176) covalent geometry : angle 0.66735 / 0.35 (14366) SS BOND : bond 0.00319 / 0.21 ( 5) SS BOND : angle 1.84028 / 1.15 ( 10) hydrogen bonds : bond 0.06386 / 4.37 ( 432) hydrogen bonds : angle 4.06925 / 2.88 ( 1150) ********************** 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 66 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8329 (mt0) cc_final: 0.7889 (mt0) REVERT: A 191 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6859 (ttm170) REVERT: A 804 LYS cc_start: 0.8179 (tttp) cc_final: 0.7957 (tppt) REVERT: A 805 GLU cc_start: 0.7426 (tp30) cc_final: 0.6802 (tp30) REVERT: A 882 LEU cc_start: 0.8325 (tp) cc_final: 0.8010 (tp) REVERT: A 894 ASP cc_start: 0.6883 (t0) cc_final: 0.6447 (t0) REVERT: A 895 GLU cc_start: 0.6743 (mp0) cc_final: 0.6009 (pm20) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.7697 time to fit residues: 50.6731 Evaluate side-chains 63 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 839 GLU 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 30 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4325 r_free = 0.4325 target = 0.205288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.158042 restraints weight = 9646.283| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.83 r_work: 0.3368 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10181 Z= 0.130 Angle : 0.577 7.638 14376 Z= 0.307 Chirality : 0.040 0.285 1653 Planarity : 0.004 0.044 1420 Dihedral : 21.704 164.042 2698 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.81 % Allowed : 13.07 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 898 helix: 1.45 (0.26), residues: 397 sheet: -0.31 (0.61), residues: 79 loop : -0.54 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1048 TYR 0.021 0.002 TYR A 698 PHE 0.027 0.002 PHE A 76 TRP 0.009 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (10176) covalent geometry : angle 0.57497 / 0.31 (14366) SS BOND : bond 0.00198 / 0.12 ( 5) SS BOND : angle 1.76190 / 1.09 ( 10) hydrogen bonds : bond 0.05616 / 3.79 ( 432) hydrogen bonds : angle 3.88730 / 2.75 ( 1150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3372.46 seconds wall clock time: 58 minutes 15.71 seconds (3495.71 seconds total)