Starting phenix.real_space_refine on Fri Sep 11 14:40:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2q_27146/09_2026/8d2q_27146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2q_27146/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2q_27146/09_2026/8d2q_27146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2q_27146/09_2026/8d2q_27146.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2q_27146/09_2026/8d2q_27146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2q_27146/09_2026/8d2q_27146.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2q_27146/09_2026/8d2q_27146.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2q_27146/09_2026/8d2q_27146.cif" } 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-2.2.1-6174/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: {'RNAv2': 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: 2.71, per 1000 atoms: 0.28 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: 0.95 Conformation dependent library (CDL) restraints added in 294.2 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: 1.25 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: 2.43 Time building geometry restraints manager: 1.27 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: 13953 2.87 - 5.75: 356 5.75 - 8.62: 42 8.62 - 11.50: 10 11.50 - 14.37: 5 Bond angle restraints: 14366 Sorted by residual: angle pdb=" C3' A B 12 " pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 119.70 133.24 -13.54 1.20e+00 6.94e-01 1.27e+02 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=" 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: 5465 31.09 - 62.17: 531 62.17 - 93.26: 110 93.26 - 124.34: 1 124.34 - 155.43: 4 Dihedral angle restraints: 6111 sinusoidal: 3495 harmonic: 2616 Sorted by residual: dihedral pdb=" C4' C B 11 " pdb=" C3' C B 11 " pdb=" C2' C B 11 " pdb=" C1' C B 11 " ideal model delta sinusoidal sigma weight residual 36.34 -38.95 75.30 1 3.10e+00 1.04e-01 7.45e+02 dihedral pdb=" C4' A B 40 " pdb=" C3' A B 40 " pdb=" C2' A B 40 " pdb=" C1' A B 40 " ideal model delta sinusoidal sigma weight residual 36.35 -37.76 74.10 1 3.10e+00 1.04e-01 7.25e+02 dihedral pdb=" C4' C B 96 " pdb=" C3' C B 96 " pdb=" C2' C B 96 " pdb=" C1' C B 96 " ideal model delta sinusoidal sigma weight residual 36.34 -37.61 73.95 1 3.10e+00 1.04e-01 7.23e+02 ... (remaining 6108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1440 0.099 - 0.198: 109 0.198 - 0.298: 90 0.298 - 0.397: 11 0.397 - 0.496: 3 Chirality restraints: 1653 Sorted by residual: chirality pdb=" C2' C B 96 " pdb=" C3' C B 96 " pdb=" O2' C B 96 " pdb=" C1' C B 96 " both_signs ideal model delta sigma weight residual False -2.79 -2.29 -0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" P A B 12 " pdb=" OP1 A B 12 " pdb=" OP2 A B 12 " pdb=" O5' A B 12 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" P C B 96 " pdb=" OP1 C B 96 " pdb=" OP2 C B 96 " pdb=" O5' C B 96 " both_signs ideal model delta sigma weight residual True 2.17 -2.57 -0.40 2.00e-01 2.50e+01 4.02e+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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- 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= 0.383 Angle : 1.075 14.373 14376 Z= 0.598 Chirality : 0.082 0.496 1653 Planarity : 0.009 0.115 1420 Dihedral : 21.798 155.427 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 0.00632 / 0.38 (10176) covalent geometry : angle 1.07336 / 0.60 (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 : 0.357 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: 0.8286 time to fit residues: 62.8705 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 : 0.295 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.207805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158535 restraints weight = 9581.600| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.62 r_work: 0.3448 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10181 Z= 0.200 Angle : 1.043 16.226 14376 Z= 0.460 Chirality : 0.104 1.263 1653 Planarity : 0.005 0.046 1420 Dihedral : 22.792 156.575 2698 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.93 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 0.011 0.001 TYR A 698 PHE 0.023 0.001 PHE A 76 TRP 0.008 0.001 TRP A 942 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (10176) covalent geometry : angle 1.04205 / 0.46 (14366) SS BOND : bond 0.00269 / 0.17 ( 5) SS BOND : angle 1.70340 / 1.01 ( 10) hydrogen bonds : bond 0.06033 / 4.22 ( 432) hydrogen bonds : angle 4.54785 / 3.20 ( 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 : 0.314 Fit side-chains REVERT: A 576 MET cc_start: 0.1781 (OUTLIER) cc_final: 0.1386 (mmt) REVERT: A 802 GLN cc_start: 0.7081 (tp40) cc_final: 0.6492 (tt0) REVERT: A 804 LYS cc_start: 0.8091 (tttp) cc_final: 0.7853 (tppt) outliers start: 5 outliers final: 0 residues processed: 64 average time/residue: 0.6889 time to fit residues: 46.9362 Evaluate side-chains 62 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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: 10.0000 chunk 84 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.204118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155221 restraints weight = 9468.511| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.85 r_work: 0.3341 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10181 Z= 0.234 Angle : 0.924 16.059 14376 Z= 0.414 Chirality : 0.083 1.249 1653 Planarity : 0.006 0.044 1420 Dihedral : 22.752 158.240 2698 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.21 % Allowed : 6.47 % Favored : 92.32 % 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: -0.04 (0.27), residues: 898 helix: 0.84 (0.26), residues: 396 sheet: -0.21 (0.55), residues: 79 loop : -0.78 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1048 TYR 0.023 0.002 TYR A 698 PHE 0.029 0.002 PHE A1086 TRP 0.013 0.002 TRP A 145 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (10176) covalent geometry : angle 0.92386 / 0.41 (14366) SS BOND : bond 0.00292 / 0.20 ( 5) SS BOND : angle 1.54052 / 0.97 ( 10) hydrogen bonds : bond 0.06663 / 4.64 ( 432) hydrogen bonds : angle 4.28183 / 3.01 ( 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 68 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.1969 (OUTLIER) cc_final: 0.1692 (mmt) REVERT: A 804 LYS cc_start: 0.8063 (tttp) cc_final: 0.7836 (tppt) REVERT: A 805 GLU cc_start: 0.7246 (tp30) cc_final: 0.6626 (tp30) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.6880 time to fit residues: 46.9887 Evaluate side-chains 59 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4332 r_free = 0.4332 target = 0.206017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158514 restraints weight = 9591.187| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.89 r_work: 0.3374 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1597 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= 0.170 Angle : 0.830 15.986 14376 Z= 0.373 Chirality : 0.078 1.239 1653 Planarity : 0.005 0.054 1420 Dihedral : 22.604 158.523 2698 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.21 % Allowed : 8.63 % 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 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: 0.23 (0.27), residues: 898 helix: 1.15 (0.26), residues: 397 sheet: -0.21 (0.57), residues: 79 loop : -0.70 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1048 TYR 0.017 0.001 TYR A 698 PHE 0.025 0.001 PHE A 76 TRP 0.006 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (10176) covalent geometry : angle 0.82974 / 0.37 (14366) SS BOND : bond 0.00214 / 0.14 ( 5) SS BOND : angle 1.54396 / 0.96 ( 10) hydrogen bonds : bond 0.05884 / 4.02 ( 432) hydrogen bonds : angle 4.06714 / 2.87 ( 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 68 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8222 (mt0) cc_final: 0.7814 (mt0) REVERT: A 191 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6657 (ttm170) REVERT: A 576 MET cc_start: 0.1945 (OUTLIER) cc_final: 0.1693 (mmt) REVERT: A 802 GLN cc_start: 0.6924 (tp-100) cc_final: 0.6610 (tt0) REVERT: A 805 GLU cc_start: 0.7242 (tp30) cc_final: 0.6609 (tp30) REVERT: A 895 GLU cc_start: 0.6600 (mp0) cc_final: 0.6114 (pm20) outliers start: 9 outliers final: 3 residues processed: 63 average time/residue: 0.7305 time to fit residues: 48.8886 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 : 0.313 ------------------------------------------------------------------------------- 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 258 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 576 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.206006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157368 restraints weight = 9563.327| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.94 r_work: 0.3366 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10181 Z= 0.168 Angle : 0.814 16.529 14376 Z= 0.366 Chirality : 0.075 1.361 1653 Planarity : 0.005 0.040 1420 Dihedral : 22.523 159.298 2698 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.89 % Allowed : 9.16 % 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: 0.43 (0.27), residues: 898 helix: 1.34 (0.26), residues: 396 sheet: -0.21 (0.58), residues: 79 loop : -0.60 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1048 TYR 0.021 0.002 TYR A 698 PHE 0.025 0.001 PHE A 76 TRP 0.008 0.001 TRP A 145 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (10176) covalent geometry : angle 0.81305 / 0.37 (14366) SS BOND : bond 0.00241 / 0.16 ( 5) SS BOND : angle 1.59593 / 0.99 ( 10) hydrogen bonds : bond 0.05768 / 3.96 ( 432) hydrogen bonds : angle 3.96258 / 2.79 ( 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 74 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8235 (mt0) cc_final: 0.7820 (mt0) REVERT: A 191 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6706 (ttm170) REVERT: A 689 VAL cc_start: 0.7864 (t) cc_final: 0.7457 (t) REVERT: A 802 GLN cc_start: 0.6953 (tp-100) cc_final: 0.6616 (tt0) REVERT: A 805 GLU cc_start: 0.7281 (tp30) cc_final: 0.6639 (tp30) REVERT: A 895 GLU cc_start: 0.6661 (mp0) cc_final: 0.6105 (pm20) outliers start: 14 outliers final: 6 residues processed: 68 average time/residue: 0.7111 time to fit residues: 51.2956 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 : 0.322 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.202970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154821 restraints weight = 9520.100| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.84 r_work: 0.3320 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10181 Z= 0.264 Angle : 0.937 15.715 14376 Z= 0.420 Chirality : 0.082 1.313 1653 Planarity : 0.006 0.054 1420 Dihedral : 22.498 159.964 2698 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.16 % Allowed : 10.38 % Favored : 87.47 % 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: 0.18 (0.27), residues: 898 helix: 1.09 (0.26), residues: 398 sheet: -0.38 (0.58), residues: 79 loop : -0.67 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1048 TYR 0.028 0.002 TYR A 698 PHE 0.029 0.002 PHE A 76 TRP 0.013 0.002 TRP A 145 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.26 (10176) covalent geometry : angle 0.93630 / 0.42 (14366) SS BOND : bond 0.00346 / 0.23 ( 5) SS BOND : angle 1.73715 / 1.10 ( 10) hydrogen bonds : bond 0.06756 / 4.66 ( 432) hydrogen bonds : angle 4.15480 / 2.92 ( 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: 16 poor density : 59 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8275 (mt0) cc_final: 0.7822 (mt0) REVERT: A 191 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6748 (ttm170) REVERT: A 802 GLN cc_start: 0.6953 (tp-100) cc_final: 0.6657 (tt0) REVERT: A 805 GLU cc_start: 0.7205 (tp30) cc_final: 0.6596 (tp30) REVERT: A 894 ASP cc_start: 0.6627 (t0) cc_final: 0.6223 (t0) REVERT: A 895 GLU cc_start: 0.6712 (mp0) cc_final: 0.6132 (pm20) outliers start: 16 outliers final: 8 residues processed: 68 average time/residue: 0.7253 time to fit residues: 52.4718 Evaluate side-chains 67 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.205354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157981 restraints weight = 9490.932| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.75 r_work: 0.3371 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10181 Z= 0.169 Angle : 0.823 15.761 14376 Z= 0.370 Chirality : 0.074 1.291 1653 Planarity : 0.005 0.042 1420 Dihedral : 22.478 159.550 2698 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.62 % Allowed : 11.59 % Favored : 86.79 % 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: -0.34 (0.59), residues: 79 loop : -0.60 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1048 TYR 0.020 0.002 TYR A 698 PHE 0.026 0.002 PHE A 76 TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (10176) covalent geometry : angle 0.82163 / 0.37 (14366) SS BOND : bond 0.00250 / 0.16 ( 5) SS BOND : angle 1.71479 / 1.07 ( 10) hydrogen bonds : bond 0.05868 / 4.02 ( 432) hydrogen bonds : angle 3.98954 / 2.81 ( 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: 12 poor density : 60 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8213 (mt0) cc_final: 0.7764 (mt0) REVERT: A 191 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6748 (ttm170) REVERT: A 802 GLN cc_start: 0.6967 (tp-100) cc_final: 0.6671 (tt0) REVERT: A 805 GLU cc_start: 0.7240 (tp30) cc_final: 0.6632 (tp30) REVERT: A 894 ASP cc_start: 0.6651 (t0) cc_final: 0.6321 (t0) REVERT: A 895 GLU cc_start: 0.6528 (mp0) cc_final: 0.6021 (pm20) outliers start: 12 outliers final: 5 residues processed: 67 average time/residue: 0.7678 time to fit residues: 54.5742 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 : 0.313 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 40 optimal weight: 0.0470 chunk 92 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 overall best weight: 2.1282 ------------------------------------------------------------------------------- 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 = 0.203991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156439 restraints weight = 9474.598| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.84 r_work: 0.3335 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10181 Z= 0.215 Angle : 0.865 15.089 14376 Z= 0.389 Chirality : 0.076 1.294 1653 Planarity : 0.005 0.051 1420 Dihedral : 22.463 160.366 2698 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.75 % Allowed : 12.13 % 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: 0.32 (0.27), residues: 898 helix: 1.25 (0.26), residues: 398 sheet: -0.41 (0.59), residues: 79 loop : -0.63 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1048 TYR 0.025 0.002 TYR A 698 PHE 0.027 0.002 PHE A 76 TRP 0.011 0.001 TRP A 145 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (10176) covalent geometry : angle 0.86436 / 0.39 (14366) SS BOND : bond 0.00290 / 0.19 ( 5) SS BOND : angle 1.77316 / 1.11 ( 10) hydrogen bonds : bond 0.06343 / 4.32 ( 432) hydrogen bonds : angle 4.05862 / 2.87 ( 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 71 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8247 (mt0) cc_final: 0.7824 (mt0) REVERT: A 191 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6792 (ttm170) REVERT: A 802 GLN cc_start: 0.6977 (tp-100) cc_final: 0.6645 (tt0) REVERT: A 805 GLU cc_start: 0.7236 (tp30) cc_final: 0.6614 (tp30) REVERT: A 894 ASP cc_start: 0.6745 (t0) cc_final: 0.6420 (t0) REVERT: A 895 GLU cc_start: 0.6607 (mp0) cc_final: 0.6023 (pm20) outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.7991 time to fit residues: 54.1137 Evaluate side-chains 63 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.4980 chunk 37 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.206274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158112 restraints weight = 9529.792| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.74 r_work: 0.3390 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2105 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= 0.160 Angle : 0.795 14.962 14376 Z= 0.359 Chirality : 0.072 1.282 1653 Planarity : 0.004 0.050 1420 Dihedral : 22.460 159.934 2698 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.08 % Allowed : 12.94 % 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: 0.49 (0.28), residues: 898 helix: 1.44 (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 ARG 0.014 0.000 ARG A1048 TYR 0.020 0.002 TYR A 698 PHE 0.025 0.002 PHE A 76 TRP 0.008 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (10176) covalent geometry : angle 0.79362 / 0.36 (14366) SS BOND : bond 0.00238 / 0.15 ( 5) SS BOND : angle 1.73765 / 1.08 ( 10) hydrogen bonds : bond 0.05716 / 3.88 ( 432) hydrogen bonds : angle 3.92931 / 2.79 ( 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: 8 poor density : 57 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8200 (mt0) cc_final: 0.7780 (mt0) REVERT: A 802 GLN cc_start: 0.6954 (tp-100) cc_final: 0.6640 (tt0) REVERT: A 805 GLU cc_start: 0.7243 (tp30) cc_final: 0.6627 (tp30) REVERT: A 894 ASP cc_start: 0.6645 (t0) cc_final: 0.6363 (t0) REVERT: A 895 GLU cc_start: 0.6505 (mp0) cc_final: 0.5937 (pm20) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.7410 time to fit residues: 47.1882 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 97 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.204235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155770 restraints weight = 9388.260| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.78 r_work: 0.3348 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2191 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= 0.214 Angle : 0.851 14.163 14376 Z= 0.384 Chirality : 0.075 1.243 1653 Planarity : 0.005 0.064 1420 Dihedral : 22.456 160.718 2698 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.21 % Allowed : 12.67 % 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: 0.40 (0.28), residues: 898 helix: 1.35 (0.26), residues: 398 sheet: -0.42 (0.59), residues: 79 loop : -0.61 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1048 TYR 0.025 0.002 TYR A 698 PHE 0.028 0.002 PHE A 76 TRP 0.012 0.001 TRP A 145 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (10176) covalent geometry : angle 0.84975 / 0.38 (14366) SS BOND : bond 0.00290 / 0.20 ( 5) SS BOND : angle 1.78694 / 1.11 ( 10) hydrogen bonds : bond 0.06223 / 4.24 ( 432) hydrogen bonds : angle 4.02177 / 2.85 ( 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 65 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8245 (mt0) cc_final: 0.7823 (mt0) REVERT: A 802 GLN cc_start: 0.6953 (tp-100) cc_final: 0.6634 (tt0) REVERT: A 805 GLU cc_start: 0.7265 (tp30) cc_final: 0.6643 (tp30) REVERT: A 894 ASP cc_start: 0.6630 (t0) cc_final: 0.6359 (t0) REVERT: A 895 GLU cc_start: 0.6586 (mp0) cc_final: 0.6020 (pm20) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.7538 time to fit residues: 48.0599 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 30 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.207088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157926 restraints weight = 9577.217| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.98 r_work: 0.3379 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10181 Z= 0.148 Angle : 0.777 14.564 14376 Z= 0.352 Chirality : 0.070 1.260 1653 Planarity : 0.004 0.067 1420 Dihedral : 22.449 160.121 2698 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.67 % Allowed : 13.48 % 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 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: 0.55 (0.28), residues: 898 helix: 1.48 (0.27), residues: 397 sheet: -0.29 (0.62), residues: 79 loop : -0.56 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 923 TYR 0.017 0.001 TYR A 698 PHE 0.024 0.001 PHE A 76 TRP 0.009 0.001 TRP A 161 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (10176) covalent geometry : angle 0.77582 / 0.35 (14366) SS BOND : bond 0.00189 / 0.12 ( 5) SS BOND : angle 1.72787 / 1.07 ( 10) hydrogen bonds : bond 0.05613 / 3.78 ( 432) hydrogen bonds : angle 3.88107 / 2.76 ( 1150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.68 seconds wall clock time: 55 minutes 20.19 seconds (3320.19 seconds total)