Starting phenix.real_space_refine on Thu Jul 2 12:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2o_27144/07_2026/8d2o_27144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2o_27144/07_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_27144/07_2026/8d2o_27144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2o_27144/07_2026/8d2o_27144.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2o_27144/07_2026/8d2o_27144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2o_27144/07_2026/8d2o_27144.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d2o_27144/07_2026/8d2o_27144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2o_27144/07_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-dev-6108/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: {'RNA': 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: 2.10, per 1000 atoms: 0.25 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: 1.10 Conformation dependent library (CDL) restraints added in 281.3 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: 1.13 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: 1.78 Time building geometry restraints manager: 1.35 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: 12218 2.16 - 4.32: 369 4.32 - 6.48: 51 6.48 - 8.64: 15 8.64 - 10.80: 2 Bond angle restraints: 12655 Sorted by residual: 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=" 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 angle pdb=" O4' DG T 17 " pdb=" C1' DG T 17 " pdb=" N9 DG T 17 " ideal model delta sigma weight residual 108.00 111.49 -3.49 7.00e-01 2.04e+00 2.48e+01 angle pdb=" O4 DT X 4 " pdb=" C4 DT X 4 " pdb=" C5 DT X 4 " ideal model delta sigma weight residual 124.90 121.57 3.33 7.00e-01 2.04e+00 2.27e+01 angle pdb=" C3' G B 95 " pdb=" O3' G B 95 " pdb=" P C B 96 " ideal model delta sigma weight residual 120.20 127.33 -7.13 1.50e+00 4.44e-01 2.26e+01 ... (remaining 12650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 4895 34.19 - 68.39: 363 68.39 - 102.58: 39 102.58 - 136.77: 2 136.77 - 170.96: 4 Dihedral angle restraints: 5303 sinusoidal: 3150 harmonic: 2153 Sorted by residual: dihedral pdb=" O4' C B 96 " pdb=" C1' C B 96 " pdb=" N1 C B 96 " pdb=" C2 C B 96 " ideal model delta sinusoidal sigma weight residual -128.00 -55.68 -72.32 1 1.70e+01 3.46e-03 2.31e+01 dihedral pdb=" CA ARG A1091 " pdb=" C ARG A1091 " pdb=" N ALA A1092 " pdb=" CA ALA A1092 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLN A 511 " pdb=" C GLN A 511 " pdb=" N SER A 512 " pdb=" CA SER A 512 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1293 0.070 - 0.141: 166 0.141 - 0.211: 12 0.211 - 0.281: 3 0.281 - 0.352: 3 Chirality restraints: 1477 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3' G B 95 " pdb=" C4' G B 95 " pdb=" O3' G B 95 " pdb=" C2' G B 95 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C3' A B 12 " pdb=" C4' A B 12 " pdb=" O3' A B 12 " pdb=" C2' A B 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.29 2.00e-01 2.50e+01 2.16e+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: 2.850 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- 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= 0.319 Angle : 0.875 10.801 12655 Z= 0.527 Chirality : 0.049 0.352 1477 Planarity : 0.009 0.124 1187 Dihedral : 20.665 170.963 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 0.00490 / 0.32 ( 8903) covalent geometry : angle 0.87536 / 0.53 (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 : 0.329 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: 0.8127 time to fit residues: 54.6197 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 : 0.255 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.4024 r_free = 0.4024 target = 0.177698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138620 restraints weight = 8993.116| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.44 r_work: 0.3317 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8903 Z= 0.205 Angle : 0.632 6.528 12655 Z= 0.337 Chirality : 0.043 0.212 1477 Planarity : 0.006 0.068 1187 Dihedral : 22.085 159.253 2529 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.81 % Allowed : 6.43 % Favored : 91.76 % 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: -0.06 (0.29), residues: 739 helix: 0.90 (0.28), residues: 326 sheet: -0.04 (0.55), residues: 83 loop : -0.97 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.023 0.002 TYR A 698 PHE 0.006 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 0.00422 / 0.20 ( 8903) covalent geometry : angle 0.63230 / 0.34 (12655) hydrogen bonds : bond 0.05541 / 3.83 ( 380) hydrogen bonds : angle 4.28209 / 3.09 ( 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 : 0.258 Fit side-chains REVERT: A 86 MET cc_start: 0.8139 (mtt) cc_final: 0.7932 (mtp) REVERT: A 125 ARG cc_start: 0.7494 (mtp85) cc_final: 0.7094 (mtp180) REVERT: A 162 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6282 (mt-10) REVERT: A 1028 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6913 (mmp) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.8175 time to fit residues: 48.0810 Evaluate side-chains 49 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU 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: 4.9990 chunk 2 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 0.0020 chunk 40 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3910 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.177640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138276 restraints weight = 8944.948| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.32 r_work: 0.3338 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8903 Z= 0.165 Angle : 0.579 7.718 12655 Z= 0.314 Chirality : 0.041 0.219 1477 Planarity : 0.006 0.121 1187 Dihedral : 22.025 158.800 2529 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.98 % Allowed : 10.05 % Favored : 87.97 % 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: 0.46 (0.29), residues: 739 helix: 1.41 (0.29), residues: 328 sheet: -0.04 (0.56), residues: 83 loop : -0.71 (0.29), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1048 TYR 0.017 0.002 TYR A 986 PHE 0.006 0.001 PHE A 730 TRP 0.009 0.001 TRP A 942 HIS 0.003 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 ( 8903) covalent geometry : angle 0.57934 / 0.31 (12655) hydrogen bonds : bond 0.05196 / 3.56 ( 380) hydrogen bonds : angle 4.04217 / 2.92 ( 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 56 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.269 Fit side-chains REVERT: A 14 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8077 (mtm-85) REVERT: A 125 ARG cc_start: 0.7492 (mtp85) cc_final: 0.7052 (mtp180) REVERT: A 162 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6233 (mt-10) REVERT: A 815 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 1028 MET cc_start: 0.7634 (ptp) cc_final: 0.6927 (mmp) outliers start: 12 outliers final: 4 residues processed: 53 average time/residue: 0.7471 time to fit residues: 41.7356 Evaluate side-chains 49 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 815 ILE 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: 7.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.175154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135262 restraints weight = 9058.627| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.43 r_work: 0.3286 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8903 Z= 0.219 Angle : 0.622 6.750 12655 Z= 0.332 Chirality : 0.043 0.219 1477 Planarity : 0.006 0.106 1187 Dihedral : 22.018 156.936 2529 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.62 % Allowed : 10.54 % Favored : 85.83 % 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: 0.46 (0.29), residues: 739 helix: 1.46 (0.29), residues: 328 sheet: -0.32 (0.54), residues: 83 loop : -0.68 (0.29), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.020 0.002 TYR A 986 PHE 0.007 0.001 PHE A 730 TRP 0.009 0.002 TRP A 942 HIS 0.007 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 ( 8903) covalent geometry : angle 0.62220 / 0.33 (12655) hydrogen bonds : bond 0.05455 / 3.81 ( 380) hydrogen bonds : angle 4.04045 / 2.91 ( 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 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.263 Fit side-chains REVERT: A 14 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8057 (mtm-85) REVERT: A 125 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7086 (mtp180) REVERT: A 482 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: A 684 THR cc_start: 0.5104 (OUTLIER) cc_final: 0.4747 (p) REVERT: A 815 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 904 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6392 (ptt-90) REVERT: A 1028 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6975 (mmp) outliers start: 22 outliers final: 8 residues processed: 60 average time/residue: 0.7139 time to fit residues: 45.2066 Evaluate side-chains 58 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 1028 MET 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: 4.9990 chunk 69 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.178337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139353 restraints weight = 9142.351| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.20 r_work: 0.3371 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8903 Z= 0.127 Angle : 0.547 6.983 12655 Z= 0.297 Chirality : 0.039 0.235 1477 Planarity : 0.004 0.039 1187 Dihedral : 21.941 157.308 2529 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.47 % Allowed : 13.18 % Favored : 84.35 % 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: 0.74 (0.30), residues: 739 helix: 1.68 (0.29), residues: 328 sheet: -0.26 (0.55), residues: 83 loop : -0.49 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1048 TYR 0.014 0.002 TYR A 986 PHE 0.006 0.001 PHE A 730 TRP 0.007 0.001 TRP A 141 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 8903) covalent geometry : angle 0.54710 / 0.30 (12655) hydrogen bonds : bond 0.04728 / 3.24 ( 380) hydrogen bonds : angle 3.87362 / 2.80 ( 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: 15 poor density : 48 time to evaluate : 0.265 Fit side-chains REVERT: A 14 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8052 (mtm-85) REVERT: A 125 ARG cc_start: 0.7495 (mtp85) cc_final: 0.7055 (mtp180) REVERT: A 684 THR cc_start: 0.5310 (OUTLIER) cc_final: 0.4940 (p) REVERT: A 815 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 1028 MET cc_start: 0.7638 (ptp) cc_final: 0.6921 (mmp) outliers start: 15 outliers final: 5 residues processed: 61 average time/residue: 0.7300 time to fit residues: 46.9734 Evaluate side-chains 53 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.174585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134280 restraints weight = 8909.398| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.40 r_work: 0.3282 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8903 Z= 0.239 Angle : 0.634 7.666 12655 Z= 0.337 Chirality : 0.044 0.220 1477 Planarity : 0.006 0.087 1187 Dihedral : 21.962 156.099 2529 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.29 % Allowed : 13.01 % Favored : 83.69 % 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: 0.55 (0.29), residues: 739 helix: 1.54 (0.29), residues: 330 sheet: -0.35 (0.53), residues: 83 loop : -0.62 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1048 TYR 0.020 0.003 TYR A 986 PHE 0.009 0.002 PHE A 730 TRP 0.009 0.002 TRP A 854 HIS 0.005 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 ( 8903) covalent geometry : angle 0.63399 / 0.34 (12655) hydrogen bonds : bond 0.05536 / 3.82 ( 380) hydrogen bonds : angle 3.96049 / 2.86 ( 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 64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.300 Fit side-chains REVERT: A 14 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8074 (mtm-85) REVERT: A 125 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7085 (mtp85) REVERT: A 482 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: A 684 THR cc_start: 0.5172 (OUTLIER) cc_final: 0.4824 (p) REVERT: A 815 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 976 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: A 1028 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.6978 (mmp) outliers start: 20 outliers final: 10 residues processed: 58 average time/residue: 0.6800 time to fit residues: 41.8578 Evaluate side-chains 59 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 684 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 976 GLU Chi-restraints excluded: chain A residue 989 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.177143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138096 restraints weight = 9122.287| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.29 r_work: 0.3341 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8903 Z= 0.145 Angle : 0.564 9.624 12655 Z= 0.305 Chirality : 0.040 0.230 1477 Planarity : 0.006 0.125 1187 Dihedral : 21.914 156.263 2529 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.98 % Allowed : 14.99 % Favored : 83.03 % 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: 1.70 (0.29), residues: 329 sheet: -0.33 (0.54), residues: 85 loop : -0.52 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1048 TYR 0.015 0.002 TYR A 986 PHE 0.007 0.001 PHE A 730 TRP 0.007 0.001 TRP A 141 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 ( 8903) covalent geometry : angle 0.56360 / 0.30 (12655) hydrogen bonds : bond 0.04970 / 3.37 ( 380) hydrogen bonds : angle 3.83846 / 2.78 ( 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 58 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.268 Fit side-chains REVERT: A 14 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8048 (mtm-85) REVERT: A 125 ARG cc_start: 0.7546 (mtp85) cc_final: 0.7102 (mtp180) REVERT: A 147 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7914 (p) REVERT: A 482 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: A 684 THR cc_start: 0.5265 (OUTLIER) cc_final: 0.4910 (p) REVERT: A 815 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 1028 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7008 (mmp) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 0.6739 time to fit residues: 39.3927 Evaluate side-chains 59 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 147 THR Chi-restraints excluded: chain A residue 181 VAL 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 989 ILE Chi-restraints excluded: chain A residue 1028 MET 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: 9.9990 chunk 79 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 29 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.173793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133438 restraints weight = 8960.608| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.38 r_work: 0.3278 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 8903 Z= 0.265 Angle : 0.665 8.972 12655 Z= 0.352 Chirality : 0.046 0.226 1477 Planarity : 0.006 0.052 1187 Dihedral : 21.972 155.128 2529 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.64 % Allowed : 14.33 % Favored : 83.03 % 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: 0.43 (0.29), residues: 739 helix: 1.43 (0.29), residues: 331 sheet: -0.51 (0.52), residues: 85 loop : -0.65 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 137 TYR 0.021 0.003 TYR A 986 PHE 0.011 0.002 PHE A 730 TRP 0.011 0.002 TRP A 145 HIS 0.005 0.002 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.26 ( 8903) covalent geometry : angle 0.66516 / 0.35 (12655) hydrogen bonds : bond 0.05915 / 4.06 ( 380) hydrogen bonds : angle 3.97154 / 2.88 ( 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 62 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.159 Fit side-chains REVERT: A 14 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8034 (mtm-85) REVERT: A 125 ARG cc_start: 0.7570 (mtp85) cc_final: 0.7053 (mtp85) REVERT: A 190 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7741 (mm110) REVERT: A 482 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: A 684 THR cc_start: 0.5332 (OUTLIER) cc_final: 0.4965 (p) REVERT: A 815 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 904 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6655 (ptt-90) REVERT: A 976 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: A 1028 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6978 (mmp) outliers start: 16 outliers final: 7 residues processed: 57 average time/residue: 0.7092 time to fit residues: 42.7658 Evaluate side-chains 60 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 684 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 904 ARG Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1028 MET 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: 0.5980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.176521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137115 restraints weight = 8991.641| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.38 r_work: 0.3316 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8903 Z= 0.153 Angle : 0.573 8.588 12655 Z= 0.310 Chirality : 0.041 0.227 1477 Planarity : 0.005 0.084 1187 Dihedral : 21.933 155.479 2529 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.14 % Allowed : 15.16 % Favored : 82.70 % 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: 0.66 (0.30), residues: 739 helix: 1.65 (0.29), residues: 329 sheet: -0.40 (0.53), residues: 85 loop : -0.55 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1048 TYR 0.015 0.002 TYR A 986 PHE 0.007 0.001 PHE A 730 TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 8903) covalent geometry : angle 0.57328 / 0.31 (12655) hydrogen bonds : bond 0.05155 / 3.48 ( 380) hydrogen bonds : angle 3.83404 / 2.79 ( 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 62 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.266 Fit side-chains REVERT: A 14 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8041 (mtm-85) REVERT: A 125 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7071 (mtm180) REVERT: A 684 THR cc_start: 0.5321 (OUTLIER) cc_final: 0.4947 (p) REVERT: A 815 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7704 (mp) REVERT: A 976 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 1028 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6968 (mmp) outliers start: 13 outliers final: 7 residues processed: 58 average time/residue: 0.7362 time to fit residues: 45.1675 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 : 0.212 ------------------------------------------------------------------------------- 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 218 THR 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 976 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1028 MET 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: 4.9990 chunk 40 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.174872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134591 restraints weight = 8989.431| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.33 r_work: 0.3288 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8903 Z= 0.208 Angle : 0.617 9.300 12655 Z= 0.329 Chirality : 0.043 0.219 1477 Planarity : 0.006 0.104 1187 Dihedral : 21.931 155.079 2529 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.14 % Allowed : 15.16 % Favored : 82.70 % 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: 0.55 (0.30), residues: 739 helix: 1.56 (0.29), residues: 330 sheet: -0.49 (0.53), residues: 85 loop : -0.60 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1048 TYR 0.019 0.002 TYR A 986 PHE 0.008 0.001 PHE A 730 TRP 0.008 0.002 TRP A 145 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 8903) covalent geometry : angle 0.61653 / 0.33 (12655) hydrogen bonds : bond 0.05451 / 3.72 ( 380) hydrogen bonds : angle 3.86807 / 2.81 ( 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 59 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.266 Fit side-chains REVERT: A 14 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8026 (mtm-85) REVERT: A 125 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7044 (mtp180) REVERT: A 684 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.4977 (p) REVERT: A 692 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7345 (ttp80) REVERT: A 815 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 976 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: A 1028 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.6983 (mmp) REVERT: A 1048 ARG cc_start: 0.8306 (mtt90) cc_final: 0.8085 (mtt180) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.7093 time to fit residues: 41.3368 Evaluate side-chains 58 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 218 THR 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 976 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1028 MET 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: 0.8980 chunk 74 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.176127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136526 restraints weight = 9013.097| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.39 r_work: 0.3307 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1902 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= 0.162 Angle : 0.578 8.760 12655 Z= 0.312 Chirality : 0.041 0.225 1477 Planarity : 0.005 0.086 1187 Dihedral : 21.907 155.331 2529 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.98 % Allowed : 15.32 % Favored : 82.70 % 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: 0.66 (0.30), residues: 739 helix: 1.63 (0.29), residues: 330 sheet: -0.45 (0.53), residues: 85 loop : -0.52 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1048 TYR 0.017 0.002 TYR A 698 PHE 0.008 0.001 PHE A 730 TRP 0.007 0.001 TRP A 141 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 8903) covalent geometry : angle 0.57765 / 0.31 (12655) hydrogen bonds : bond 0.05118 / 3.48 ( 380) hydrogen bonds : angle 3.81226 / 2.77 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3145.79 seconds wall clock time: 54 minutes 26.78 seconds (3266.78 seconds total)