Starting phenix.real_space_refine on Fri Sep 11 08:32:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2o_27144/09_2026/8d2o_27144.cif" } resolution = 2.66 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= 0.005 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 122 5.49 5 Mg 5 5.21 5 S 10 5.16 5 C 4878 2.51 5 N 1567 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 8471 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5872 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 44, 'TRANS': 699} Chain breaks: 4 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: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1855 Classifications: {'RNAv2': 87} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 10, 'rna3p': 76} Chain breaks: 2 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: "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: "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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.39, per 1000 atoms: 0.28 Number of scatterers: 8471 At special positions: 0 Unit cell: (91.575, 94.875, 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 10 16.00 P 122 15.00 Mg 5 11.99 O 1889 8.00 N 1567 7.00 C 4878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.94 Conformation dependent library (CDL) restraints added in 219.0 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 44.7% alpha, 12.8% beta 43 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 1.35 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: 3.544A 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 685 through 703 Processing helix chain 'A' and resid 713 through 722 removed outlier: 3.833A pdb=" N GLU A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.708A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 746 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 748 through 759 removed outlier: 3.796A pdb=" N THR A 759 " --> pdb=" O VAL A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 782 removed outlier: 4.112A pdb=" N SER A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 removed outlier: 3.688A 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: 3.793A pdb=" N MET A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) removed outlier: 4.245A 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: 6.172A pdb=" N ILE A 513 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE A 710 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 515 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 30 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE A 39 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA3, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA4, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA5, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA6, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.726A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.798A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.16 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: 2029 1.33 - 1.46: 2676 1.46 - 1.58: 3942 1.58 - 1.70: 241 1.70 - 1.82: 15 Bond restraints: 8903 Sorted by residual: bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" C3' DC D 35 " pdb=" O3' DC D 35 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" C3' DA D 36 " pdb=" O3' DA D 36 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C3' DA D 29 " pdb=" C2' DA D 29 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C1' DC T 14 " pdb=" N1 DC T 14 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 ... (remaining 8898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12010 2.16 - 4.32: 557 4.32 - 6.48: 68 6.48 - 8.64: 18 8.64 - 10.80: 2 Bond angle restraints: 12655 Sorted by residual: angle pdb=" C3' G B 95 " pdb=" O3' G B 95 " pdb=" P C B 96 " ideal model delta sigma weight residual 119.70 127.33 -7.63 1.20e+00 6.94e-01 4.04e+01 angle pdb=" C3' G B 14 " pdb=" O3' G B 14 " pdb=" P A B 15 " ideal model delta sigma weight residual 119.70 126.39 -6.69 1.20e+00 6.94e-01 3.11e+01 angle pdb=" N3 DT X 4 " pdb=" C4 DT X 4 " pdb=" O4 DT X 4 " ideal model delta sigma weight residual 119.90 123.21 -3.31 6.00e-01 2.78e+00 3.04e+01 angle pdb=" C3' A B 12 " pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 119.70 126.22 -6.52 1.20e+00 6.94e-01 2.95e+01 angle pdb=" CA PRO A1087 " pdb=" N PRO A1087 " pdb=" CD PRO A1087 " ideal model delta sigma weight residual 111.50 104.00 7.50 1.40e+00 5.10e-01 2.87e+01 ... (remaining 12650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 4788 34.19 - 68.39: 469 68.39 - 102.58: 41 102.58 - 136.77: 1 136.77 - 170.96: 4 Dihedral angle restraints: 5303 sinusoidal: 3150 harmonic: 2153 Sorted by residual: dihedral pdb=" C4' A B 39 " pdb=" C3' A B 39 " pdb=" C2' A B 39 " pdb=" C1' A B 39 " ideal model delta sinusoidal sigma weight residual 36.34 -40.87 77.22 1 3.10e+00 1.04e-01 7.78e+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 36.34 -37.52 73.86 1 3.10e+00 1.04e-01 7.21e+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 36.35 -36.74 73.08 1 3.10e+00 1.04e-01 7.08e+02 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1240 0.080 - 0.160: 123 0.160 - 0.239: 72 0.239 - 0.319: 35 0.319 - 0.399: 7 Chirality restraints: 1477 Sorted by residual: 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 3.98e+00 chirality pdb=" P A B 13 " pdb=" OP1 A B 13 " pdb=" OP2 A B 13 " pdb=" O5' A B 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.55 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C2' A B 39 " pdb=" C3' A B 39 " pdb=" O2' A B 39 " pdb=" C1' A B 39 " both_signs ideal model delta sigma weight residual False -2.79 -2.42 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 1474 not shown) Planarity restraints: 1187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 9 " 0.081 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO A 10 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 14 " 0.217 9.50e-02 1.11e+02 9.78e-02 6.63e+00 pdb=" NE ARG A 14 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 14 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 14 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 14 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 97 " 0.027 2.00e-02 2.50e+03 1.39e-02 5.84e+00 pdb=" N9 G B 97 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G B 97 " -0.026 2.00e-02 2.50e+03 pdb=" N7 G B 97 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G B 97 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G B 97 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 97 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G B 97 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G B 97 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G B 97 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G B 97 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 97 " 0.013 2.00e-02 2.50e+03 ... (remaining 1184 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 460 2.72 - 3.26: 7425 3.26 - 3.81: 16411 3.81 - 4.35: 19740 4.35 - 4.90: 29586 Nonbonded interactions: 73622 Sorted by model distance: nonbonded pdb=" ND1 HIS A 750 " pdb="MG MG A1201 " model vdw 2.174 2.250 nonbonded pdb=" OG1 THR A 504 " pdb=" OH TYR A 698 " model vdw 2.268 3.040 nonbonded pdb=" OG SER A 59 " pdb=" OP1 C B 17 " model vdw 2.306 3.040 nonbonded pdb=" O LEU A 842 " pdb=" O2' C B 26 " model vdw 2.320 3.040 nonbonded pdb=" O2' A B 40 " pdb=" O4' A B 41 " model vdw 2.321 3.040 ... (remaining 73617 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: 2.390 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.005 0.078 8903 Z= 0.322 Angle : 0.975 10.801 12655 Z= 0.543 Chirality : 0.082 0.399 1477 Planarity : 0.009 0.124 1187 Dihedral : 22.204 170.963 3907 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: -1.19 (0.27), residues: 739 helix: -0.38 (0.26), residues: 322 sheet: -0.23 (0.54), residues: 83 loop : -1.26 (0.28), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 14 TYR 0.014 0.003 TYR A 986 PHE 0.016 0.002 PHE A 76 TRP 0.021 0.002 TRP A1128 HIS 0.012 0.002 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.32 ( 8903) covalent geometry : angle 0.97490 / 0.54 (12655) hydrogen bonds : bond 0.07399 / 5.87 ( 380) hydrogen bonds : angle 5.16348 / 3.72 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.291 Fit side-chains REVERT: A 86 MET cc_start: 0.7800 (mtt) cc_final: 0.7579 (mtp) REVERT: A 98 ASP cc_start: 0.7976 (m-30) cc_final: 0.7645 (m-30) REVERT: A 125 ARG cc_start: 0.7287 (mtp85) cc_final: 0.7056 (mtp180) REVERT: A 1025 ASP cc_start: 0.7204 (m-30) cc_final: 0.6889 (m-30) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.7941 time to fit residues: 53.4151 Evaluate side-chains 42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.179118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139484 restraints weight = 8934.638| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.41 r_work: 0.3332 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8903 Z= 0.244 Angle : 1.102 17.857 12655 Z= 0.484 Chirality : 0.117 1.705 1477 Planarity : 0.006 0.069 1187 Dihedral : 22.919 175.189 2529 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.81 % Allowed : 6.26 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: -0.11 (0.28), residues: 739 helix: 0.83 (0.28), residues: 326 sheet: -0.03 (0.55), residues: 83 loop : -0.96 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 506 TYR 0.022 0.002 TYR A 698 PHE 0.007 0.001 PHE A 76 TRP 0.011 0.002 TRP A 942 HIS 0.004 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 ( 8903) covalent geometry : angle 1.10156 / 0.48 (12655) hydrogen bonds : bond 0.05635 / 3.89 ( 380) hydrogen bonds : angle 4.31812 / 3.12 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.315 Fit side-chains REVERT: A 86 MET cc_start: 0.8161 (mtt) cc_final: 0.7956 (mtp) REVERT: A 125 ARG cc_start: 0.7493 (mtp85) cc_final: 0.7089 (mtp180) REVERT: A 1028 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6862 (mmp) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.8087 time to fit residues: 47.5812 Evaluate side-chains 47 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 904 ARG Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 0.0870 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.177540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139033 restraints weight = 8876.611| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.40 r_work: 0.3309 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8903 Z= 0.237 Angle : 0.899 15.892 12655 Z= 0.406 Chirality : 0.086 1.573 1477 Planarity : 0.006 0.104 1187 Dihedral : 22.914 167.769 2529 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.64 % Allowed : 10.21 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.30 (0.29), residues: 739 helix: 1.27 (0.29), residues: 328 sheet: -0.13 (0.54), residues: 83 loop : -0.79 (0.29), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.020 0.002 TYR A 986 PHE 0.009 0.002 PHE A 881 TRP 0.010 0.002 TRP A 942 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 ( 8903) covalent geometry : angle 0.89928 / 0.41 (12655) hydrogen bonds : bond 0.05683 / 3.90 ( 380) hydrogen bonds : angle 4.11204 / 2.98 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.284 Fit side-chains REVERT: A 14 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8108 (mtm-85) REVERT: A 125 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7047 (mtp180) REVERT: A 815 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 1028 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7053 (mmm) outliers start: 16 outliers final: 8 residues processed: 55 average time/residue: 0.7249 time to fit residues: 42.2666 Evaluate side-chains 52 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.182097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142675 restraints weight = 9112.649| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.28 r_work: 0.3392 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8903 Z= 0.146 Angle : 0.772 15.977 12655 Z= 0.346 Chirality : 0.074 1.342 1477 Planarity : 0.005 0.093 1187 Dihedral : 22.739 159.669 2529 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 11.86 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.73 (0.30), residues: 739 helix: 1.67 (0.29), residues: 328 sheet: -0.21 (0.56), residues: 83 loop : -0.51 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.013 0.002 TYR A 986 PHE 0.006 0.001 PHE A 730 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 0.00287 / 0.15 ( 8903) covalent geometry : angle 0.77201 / 0.35 (12655) hydrogen bonds : bond 0.04816 / 3.31 ( 380) hydrogen bonds : angle 3.91454 / 2.85 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.267 Fit side-chains REVERT: A 14 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8104 (mtm-85) REVERT: A 125 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7046 (mtp180) REVERT: A 684 THR cc_start: 0.5318 (OUTLIER) cc_final: 0.4940 (p) REVERT: A 815 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 1028 MET cc_start: 0.7679 (ptp) cc_final: 0.7004 (mmp) outliers start: 11 outliers final: 3 residues processed: 58 average time/residue: 0.7855 time to fit residues: 47.9656 Evaluate side-chains 53 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141283 restraints weight = 9015.922| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.37 r_work: 0.3363 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8903 Z= 0.189 Angle : 0.778 11.960 12655 Z= 0.355 Chirality : 0.067 0.853 1477 Planarity : 0.005 0.039 1187 Dihedral : 22.636 157.749 2529 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.64 % Allowed : 12.85 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.77 (0.30), residues: 739 helix: 1.74 (0.29), residues: 328 sheet: -0.31 (0.55), residues: 83 loop : -0.50 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 911 TYR 0.017 0.002 TYR A 986 PHE 0.007 0.001 PHE A 730 TRP 0.007 0.001 TRP A 942 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 8903) covalent geometry : angle 0.77776 / 0.35 (12655) hydrogen bonds : bond 0.05028 / 3.47 ( 380) hydrogen bonds : angle 3.92172 / 2.84 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.265 Fit side-chains REVERT: A 14 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8030 (mtm-85) REVERT: A 125 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7094 (mtp85) REVERT: A 482 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 684 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.4993 (p) REVERT: A 815 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 1028 MET cc_start: 0.7785 (ptp) cc_final: 0.7038 (mmp) outliers start: 16 outliers final: 6 residues processed: 59 average time/residue: 0.7542 time to fit residues: 46.9031 Evaluate side-chains 52 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135212 restraints weight = 8863.788| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.39 r_work: 0.3294 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8903 Z= 0.336 Angle : 0.934 12.488 12655 Z= 0.429 Chirality : 0.075 0.817 1477 Planarity : 0.007 0.057 1187 Dihedral : 22.795 156.046 2529 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.46 % Allowed : 13.34 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.16 (0.29), residues: 739 helix: 1.16 (0.28), residues: 331 sheet: -0.57 (0.52), residues: 83 loop : -0.75 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 137 TYR 0.023 0.003 TYR A 986 PHE 0.012 0.002 PHE A 730 TRP 0.012 0.002 TRP A 145 HIS 0.007 0.002 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.34 ( 8903) covalent geometry : angle 0.93431 / 0.43 (12655) hydrogen bonds : bond 0.06480 / 4.52 ( 380) hydrogen bonds : angle 4.17331 / 3.02 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.279 Fit side-chains REVERT: A 14 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7922 (mtm-85) REVERT: A 125 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7161 (mtp85) REVERT: A 190 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7793 (mm110) REVERT: A 482 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: A 684 THR cc_start: 0.5233 (OUTLIER) cc_final: 0.4865 (p) REVERT: A 815 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7753 (mp) outliers start: 21 outliers final: 9 residues processed: 61 average time/residue: 0.7021 time to fit residues: 45.2825 Evaluate side-chains 57 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 904 ARG Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139154 restraints weight = 9055.499| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.34 r_work: 0.3344 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8903 Z= 0.191 Angle : 0.779 10.630 12655 Z= 0.362 Chirality : 0.065 0.743 1477 Planarity : 0.006 0.114 1187 Dihedral : 22.702 154.308 2529 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.98 % Allowed : 15.16 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.42 (0.30), residues: 739 helix: 1.42 (0.29), residues: 330 sheet: -0.59 (0.52), residues: 85 loop : -0.63 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.018 0.002 TYR A 986 PHE 0.007 0.001 PHE A 730 TRP 0.009 0.001 TRP A 141 HIS 0.005 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 ( 8903) covalent geometry : angle 0.77864 / 0.36 (12655) hydrogen bonds : bond 0.05485 / 3.70 ( 380) hydrogen bonds : angle 3.95321 / 2.89 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.285 Fit side-chains REVERT: A 14 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7983 (mtm-85) REVERT: A 125 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7137 (mtp180) REVERT: A 190 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7890 (mm110) REVERT: A 684 THR cc_start: 0.5211 (OUTLIER) cc_final: 0.4839 (p) REVERT: A 815 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7722 (mp) outliers start: 12 outliers final: 5 residues processed: 56 average time/residue: 0.7739 time to fit residues: 45.7262 Evaluate side-chains 57 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 73 optimal weight: 0.1980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140963 restraints weight = 8969.825| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.34 r_work: 0.3371 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8903 Z= 0.171 Angle : 0.735 9.422 12655 Z= 0.342 Chirality : 0.061 0.614 1477 Planarity : 0.005 0.092 1187 Dihedral : 22.557 157.632 2529 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.98 % Allowed : 15.16 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.58 (0.30), residues: 739 helix: 1.61 (0.29), residues: 328 sheet: -0.54 (0.53), residues: 85 loop : -0.57 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.017 0.002 TYR A 986 PHE 0.007 0.001 PHE A 730 TRP 0.008 0.001 TRP A 161 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 8903) covalent geometry : angle 0.73534 / 0.34 (12655) hydrogen bonds : bond 0.05100 / 3.45 ( 380) hydrogen bonds : angle 3.83497 / 2.80 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.208 Fit side-chains REVERT: A 14 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8018 (mtm-85) REVERT: A 125 ARG cc_start: 0.7567 (mtp85) cc_final: 0.7110 (mtm180) REVERT: A 684 THR cc_start: 0.5364 (OUTLIER) cc_final: 0.4987 (p) REVERT: A 692 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7365 (ttp80) REVERT: A 815 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7710 (mp) REVERT: A 1028 MET cc_start: 0.7706 (ptt) cc_final: 0.6895 (mmp) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.7689 time to fit residues: 48.4931 Evaluate side-chains 57 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141991 restraints weight = 8931.752| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.43 r_work: 0.3374 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8903 Z= 0.229 Angle : 0.786 8.858 12655 Z= 0.365 Chirality : 0.064 0.630 1477 Planarity : 0.005 0.055 1187 Dihedral : 22.573 158.618 2529 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.65 % Allowed : 15.82 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.47 (0.30), residues: 739 helix: 1.50 (0.29), residues: 330 sheet: -0.60 (0.53), residues: 85 loop : -0.62 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1048 TYR 0.020 0.003 TYR A 698 PHE 0.009 0.001 PHE A 730 TRP 0.008 0.002 TRP A 145 HIS 0.005 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 ( 8903) covalent geometry : angle 0.78600 / 0.37 (12655) hydrogen bonds : bond 0.05609 / 3.82 ( 380) hydrogen bonds : angle 3.89163 / 2.84 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.184 Fit side-chains REVERT: A 14 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8036 (mtm-85) REVERT: A 125 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7100 (mtp180) REVERT: A 684 THR cc_start: 0.5395 (OUTLIER) cc_final: 0.5028 (p) REVERT: A 692 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7411 (ttp80) REVERT: A 815 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7751 (mp) REVERT: A 1028 MET cc_start: 0.7676 (ptt) cc_final: 0.6937 (mmp) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.6837 time to fit residues: 38.9511 Evaluate side-chains 54 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.181272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142555 restraints weight = 8992.246| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.41 r_work: 0.3377 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8903 Z= 0.199 Angle : 0.760 8.657 12655 Z= 0.353 Chirality : 0.063 0.626 1477 Planarity : 0.006 0.117 1187 Dihedral : 22.562 159.302 2529 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.65 % Allowed : 16.14 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.50 (0.30), residues: 739 helix: 1.50 (0.29), residues: 330 sheet: -0.57 (0.53), residues: 85 loop : -0.59 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.019 0.002 TYR A 698 PHE 0.008 0.001 PHE A 730 TRP 0.007 0.001 TRP A 141 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 8903) covalent geometry : angle 0.75998 / 0.35 (12655) hydrogen bonds : bond 0.05319 / 3.64 ( 380) hydrogen bonds : angle 3.86359 / 2.82 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.227 Fit side-chains REVERT: A 14 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8037 (mtm-85) REVERT: A 125 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7106 (mtp180) REVERT: A 684 THR cc_start: 0.5503 (OUTLIER) cc_final: 0.5136 (p) REVERT: A 692 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7386 (ttp80) REVERT: A 815 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7758 (mp) REVERT: A 1028 MET cc_start: 0.7699 (ptt) cc_final: 0.6941 (mmp) REVERT: A 1048 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7918 (mtt180) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.7050 time to fit residues: 39.5481 Evaluate side-chains 55 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145089 restraints weight = 9060.284| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.40 r_work: 0.3417 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8903 Z= 0.154 Angle : 0.715 7.105 12655 Z= 0.333 Chirality : 0.060 0.584 1477 Planarity : 0.005 0.058 1187 Dihedral : 22.477 160.227 2529 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.48 % Allowed : 16.14 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % 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: 0.69 (0.30), residues: 739 helix: 1.67 (0.29), residues: 330 sheet: -0.53 (0.54), residues: 85 loop : -0.49 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.016 0.002 TYR A 698 PHE 0.007 0.001 PHE A 730 TRP 0.008 0.001 TRP A 161 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 8903) covalent geometry : angle 0.71464 / 0.33 (12655) hydrogen bonds : bond 0.04925 / 3.35 ( 380) hydrogen bonds : angle 3.78967 / 2.77 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3121.25 seconds wall clock time: 53 minutes 54.89 seconds (3234.89 seconds total)