Starting phenix.real_space_refine on Thu Mar 13 06:12:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2o_27144/03_2025/8d2o_27144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2o_27144/03_2025/8d2o_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_27144/03_2025/8d2o_27144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2o_27144/03_2025/8d2o_27144.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2o_27144/03_2025/8d2o_27144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2o_27144/03_2025/8d2o_27144.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, '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: 5.91, per 1000 atoms: 0.70 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: 2.27 Conformation dependent library (CDL) restraints added in 785.6 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: 3.47 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: 3.66 Time building geometry restraints manager: 2.67 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=" C3' G B 95 " pdb=" O3' G B 95 " ideal model delta sigma weight residual 1.427 1.464 -0.037 1.50e-02 4.44e+03 6.24e+00 bond pdb=" C3' DC D 35 " pdb=" O3' DC D 35 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.58e+00 bond pdb=" C3' DA D 36 " pdb=" O3' DA D 36 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.34e+00 bond pdb=" CB PRO A1087 " pdb=" CG PRO A1087 " ideal model delta sigma weight residual 1.506 1.584 -0.078 3.90e-02 6.57e+02 3.99e+00 bond pdb=" CG PRO A1087 " pdb=" CD PRO A1087 " ideal model delta sigma weight residual 1.512 1.459 0.053 2.70e-02 1.37e+03 3.91e+00 ... (remaining 8898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12264 2.16 - 4.32: 324 4.32 - 6.48: 50 6.48 - 8.64: 15 8.64 - 10.80: 2 Bond angle restraints: 12655 Sorted by residual: 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=" 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 angle pdb=" CG ARG A 14 " pdb=" CD ARG A 14 " pdb=" NE ARG A 14 " ideal model delta sigma weight residual 112.00 122.09 -10.09 2.20e+00 2.07e-01 2.10e+01 angle pdb=" O3' G B 14 " pdb=" C3' G B 14 " pdb=" C2' G B 14 " ideal model delta sigma weight residual 113.70 120.39 -6.69 1.50e+00 4.44e-01 1.99e+01 angle pdb=" O3' G B 95 " pdb=" C3' G B 95 " pdb=" C2' G B 95 " ideal model delta sigma weight residual 109.50 115.97 -6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 12650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 4935 34.19 - 68.39: 391 68.39 - 102.58: 39 102.58 - 136.77: 2 136.77 - 170.96: 4 Dihedral angle restraints: 5371 sinusoidal: 3218 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 5368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1306 0.070 - 0.141: 154 0.141 - 0.211: 12 0.211 - 0.281: 2 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: 1.360 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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= 0.288 Angle : 0.850 10.801 12655 Z= 0.445 Chirality : 0.048 0.352 1477 Planarity : 0.009 0.124 1187 Dihedral : 21.022 170.963 3975 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (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 TRP 0.021 0.002 TRP A1128 HIS 0.012 0.002 HIS A 749 PHE 0.016 0.002 PHE A 76 TYR 0.014 0.003 TYR A 986 ARG 0.015 0.001 ARG A 14 *********************** 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 : 0.742 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: 1.8610 time to fit residues: 125.8199 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 : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143285 restraints weight = 9005.546| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.35 r_work: 0.3401 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0992 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= 0.166 Angle : 0.544 6.896 12655 Z= 0.288 Chirality : 0.037 0.234 1477 Planarity : 0.005 0.071 1187 Dihedral : 22.288 159.123 2597 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.32 % Allowed : 6.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 739 helix: 1.08 (0.29), residues: 326 sheet: 0.00 (0.56), residues: 83 loop : -0.80 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.004 0.001 HIS A 749 PHE 0.006 0.001 PHE A 76 TYR 0.017 0.002 TYR A 698 ARG 0.005 0.000 ARG A 911 *********************** 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: 8 poor density : 54 time to evaluate : 0.691 Fit side-chains REVERT: A 116 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: A 125 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7105 (mtp180) REVERT: A 162 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6298 (mt-10) REVERT: A 1028 MET cc_start: 0.7509 (ptp) cc_final: 0.6837 (mmp) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 1.6979 time to fit residues: 105.4509 Evaluate side-chains 45 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 218 THR 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 77 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 0.0570 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.181518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142036 restraints weight = 9088.168| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.34 r_work: 0.3386 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8903 Z= 0.166 Angle : 0.529 8.250 12655 Z= 0.280 Chirality : 0.037 0.226 1477 Planarity : 0.005 0.089 1187 Dihedral : 22.184 158.393 2597 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.81 % Allowed : 9.39 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.30), residues: 739 helix: 1.64 (0.29), residues: 328 sheet: -0.02 (0.57), residues: 83 loop : -0.62 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 507 HIS 0.003 0.001 HIS A1100 PHE 0.005 0.001 PHE A 730 TYR 0.014 0.002 TYR A 698 ARG 0.014 0.000 ARG A1048 *********************** 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 59 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 1.019 Fit side-chains REVERT: A 125 ARG cc_start: 0.7526 (mtp85) cc_final: 0.7087 (mtp180) REVERT: A 815 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 1028 MET cc_start: 0.7642 (ptp) cc_final: 0.6921 (mmp) outliers start: 11 outliers final: 3 residues processed: 57 average time/residue: 1.4763 time to fit residues: 89.4243 Evaluate side-chains 50 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135267 restraints weight = 9011.877| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.44 r_work: 0.3263 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8903 Z= 0.366 Angle : 0.664 9.399 12655 Z= 0.348 Chirality : 0.044 0.225 1477 Planarity : 0.006 0.099 1187 Dihedral : 22.396 155.064 2597 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.79 % Allowed : 9.72 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.29), residues: 739 helix: 1.38 (0.29), residues: 331 sheet: -0.18 (0.55), residues: 83 loop : -0.68 (0.29), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 145 HIS 0.006 0.002 HIS A 936 PHE 0.009 0.002 PHE A 730 TYR 0.022 0.003 TYR A 986 ARG 0.011 0.001 ARG A1048 *********************** 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 70 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.780 Fit side-chains REVERT: A 14 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8033 (mtm-85) REVERT: A 125 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7098 (mtp180) REVERT: A 506 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8278 (mmm160) REVERT: A 684 THR cc_start: 0.5233 (OUTLIER) cc_final: 0.4900 (p) REVERT: A 815 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7722 (mp) REVERT: A 904 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6642 (ptt-90) REVERT: A 1028 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6994 (mmp) outliers start: 23 outliers final: 8 residues processed: 63 average time/residue: 1.5312 time to fit residues: 101.9295 Evaluate side-chains 62 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 849 THR 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 42 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136965 restraints weight = 8960.506| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.27 r_work: 0.3333 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8903 Z= 0.226 Angle : 0.576 9.648 12655 Z= 0.304 Chirality : 0.039 0.227 1477 Planarity : 0.005 0.107 1187 Dihedral : 22.248 155.628 2597 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.31 % Allowed : 12.69 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 739 helix: 1.61 (0.29), residues: 329 sheet: -0.30 (0.54), residues: 85 loop : -0.56 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 942 HIS 0.004 0.001 HIS A1100 PHE 0.007 0.001 PHE A 730 TYR 0.016 0.002 TYR A 986 ARG 0.013 0.000 ARG A1048 *********************** 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 62 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.712 Fit side-chains REVERT: A 14 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8075 (mtm-85) REVERT: A 125 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7080 (mtp180) REVERT: A 482 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: A 506 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8200 (mmm160) REVERT: A 684 THR cc_start: 0.5274 (OUTLIER) cc_final: 0.4944 (p) REVERT: A 815 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7686 (mp) REVERT: A 1028 MET cc_start: 0.7721 (ptp) cc_final: 0.6988 (mmp) outliers start: 14 outliers final: 6 residues processed: 57 average time/residue: 1.5548 time to fit residues: 93.7069 Evaluate side-chains 56 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 506 ARG 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 849 THR 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 41 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136912 restraints weight = 8973.834| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.40 r_work: 0.3318 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8903 Z= 0.227 Angle : 0.567 7.725 12655 Z= 0.299 Chirality : 0.039 0.226 1477 Planarity : 0.004 0.036 1187 Dihedral : 22.200 155.299 2597 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.46 % Allowed : 12.52 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 739 helix: 1.67 (0.29), residues: 329 sheet: -0.34 (0.54), residues: 85 loop : -0.53 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 854 HIS 0.003 0.001 HIS A1100 PHE 0.007 0.001 PHE A 730 TYR 0.016 0.002 TYR A 986 ARG 0.005 0.000 ARG A 911 *********************** 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 71 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 1.272 Fit side-chains REVERT: A 14 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8076 (mtm-85) REVERT: A 125 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7073 (mtp180) REVERT: A 147 THR cc_start: 0.8145 (m) cc_final: 0.7886 (p) REVERT: A 150 ASP cc_start: 0.7652 (m-30) cc_final: 0.7293 (m-30) REVERT: A 190 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7632 (mm110) REVERT: A 506 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8211 (mmm160) REVERT: A 684 THR cc_start: 0.5375 (OUTLIER) cc_final: 0.5029 (p) REVERT: A 815 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7678 (mp) REVERT: A 904 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6678 (ptt-90) REVERT: A 1028 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7005 (mmp) outliers start: 21 outliers final: 8 residues processed: 64 average time/residue: 1.8403 time to fit residues: 124.9573 Evaluate side-chains 62 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 506 ARG 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 849 THR Chi-restraints excluded: chain A residue 904 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.0030 chunk 40 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137884 restraints weight = 9070.406| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.42 r_work: 0.3314 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8903 Z= 0.200 Angle : 0.547 7.285 12655 Z= 0.290 Chirality : 0.038 0.230 1477 Planarity : 0.005 0.081 1187 Dihedral : 22.148 155.577 2597 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.47 % Allowed : 13.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 739 helix: 1.76 (0.29), residues: 329 sheet: -0.35 (0.54), residues: 85 loop : -0.45 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.003 0.001 HIS A1100 PHE 0.007 0.001 PHE A 730 TYR 0.015 0.002 TYR A 986 ARG 0.009 0.000 ARG A1048 *********************** 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 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.711 Fit side-chains REVERT: A 14 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8073 (mtm-85) REVERT: A 125 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7022 (mtp180) REVERT: A 190 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7615 (mm110) REVERT: A 506 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8236 (mmm160) REVERT: A 684 THR cc_start: 0.5443 (OUTLIER) cc_final: 0.5061 (p) REVERT: A 692 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7290 (ttp80) REVERT: A 815 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7678 (mp) REVERT: A 1028 MET cc_start: 0.7735 (ptp) cc_final: 0.6987 (mmp) outliers start: 15 outliers final: 8 residues processed: 62 average time/residue: 1.3940 time to fit residues: 91.9785 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 : 0.775 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 506 ARG 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 849 THR 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 7 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140840 restraints weight = 9190.577| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.31 r_work: 0.3379 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1826 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= 0.180 Angle : 0.535 7.078 12655 Z= 0.284 Chirality : 0.038 0.232 1477 Planarity : 0.004 0.053 1187 Dihedral : 22.098 155.880 2597 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 739 helix: 1.88 (0.29), residues: 328 sheet: -0.35 (0.55), residues: 85 loop : -0.43 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.003 0.001 HIS A 936 PHE 0.007 0.001 PHE A 730 TYR 0.016 0.002 TYR A 800 ARG 0.008 0.000 ARG A1048 *********************** 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 65 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.821 Fit side-chains REVERT: A 14 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8060 (mtm-85) REVERT: A 125 ARG cc_start: 0.7477 (mtp85) cc_final: 0.7266 (mtt180) REVERT: A 147 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7890 (p) REVERT: A 506 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8239 (mmm160) REVERT: A 684 THR cc_start: 0.5493 (OUTLIER) cc_final: 0.5104 (p) REVERT: A 692 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7293 (ttp80) REVERT: A 815 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7679 (mp) REVERT: A 1028 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6990 (mmp) outliers start: 16 outliers final: 9 residues processed: 58 average time/residue: 1.4365 time to fit residues: 88.4806 Evaluate side-chains 64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 147 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 506 ARG 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 849 THR 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 32 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 68 optimal weight: 0.0670 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135627 restraints weight = 9060.258| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.32 r_work: 0.3330 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2021 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= 0.320 Angle : 0.629 8.319 12655 Z= 0.329 Chirality : 0.042 0.227 1477 Planarity : 0.006 0.104 1187 Dihedral : 22.254 153.983 2597 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.80 % Allowed : 15.32 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 739 helix: 1.61 (0.29), residues: 331 sheet: -0.50 (0.54), residues: 85 loop : -0.56 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 145 HIS 0.004 0.002 HIS A1100 PHE 0.009 0.001 PHE A 730 TYR 0.020 0.002 TYR A 986 ARG 0.011 0.001 ARG A1048 *********************** 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 70 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.740 Fit side-chains REVERT: A 14 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8090 (mtm-85) REVERT: A 125 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7075 (mtp180) REVERT: A 190 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7702 (mm110) REVERT: A 506 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8289 (mmm160) REVERT: A 684 THR cc_start: 0.5719 (OUTLIER) cc_final: 0.5333 (p) REVERT: A 692 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7404 (ttp80) REVERT: A 815 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 1028 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7047 (mmp) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 1.4550 time to fit residues: 96.9738 Evaluate side-chains 65 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 697 SER 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 849 THR 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 68 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.176524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136895 restraints weight = 8980.141| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.31 r_work: 0.3340 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8903 Z= 0.261 Angle : 0.597 8.178 12655 Z= 0.315 Chirality : 0.041 0.222 1477 Planarity : 0.005 0.052 1187 Dihedral : 22.224 154.380 2597 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.80 % Allowed : 14.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 739 helix: 1.65 (0.29), residues: 330 sheet: -0.54 (0.54), residues: 85 loop : -0.56 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.004 0.001 HIS A1100 PHE 0.008 0.001 PHE A 730 TYR 0.017 0.002 TYR A 986 ARG 0.015 0.001 ARG A1048 ********************** 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 67 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 1.201 Fit side-chains REVERT: A 14 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8067 (mtm-85) REVERT: A 125 ARG cc_start: 0.7477 (mtp85) cc_final: 0.6990 (mtp180) REVERT: A 190 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7697 (mm110) REVERT: A 506 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8298 (mmm160) REVERT: A 684 THR cc_start: 0.5561 (OUTLIER) cc_final: 0.5185 (p) REVERT: A 692 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7386 (ttp80) REVERT: A 815 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 904 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6694 (ptt-90) REVERT: A 1028 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6993 (mmp) outliers start: 17 outliers final: 10 residues processed: 60 average time/residue: 1.7874 time to fit residues: 114.7216 Evaluate side-chains 64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 697 SER 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 849 THR Chi-restraints excluded: chain A residue 904 ARG 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 61 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.177020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137354 restraints weight = 9193.927| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.31 r_work: 0.3347 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8903 Z= 0.240 Angle : 0.581 7.766 12655 Z= 0.307 Chirality : 0.040 0.224 1477 Planarity : 0.004 0.038 1187 Dihedral : 22.200 154.834 2597 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.64 % Allowed : 15.32 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.30), residues: 739 helix: 1.70 (0.29), residues: 330 sheet: -0.53 (0.55), residues: 85 loop : -0.53 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.004 0.001 HIS A 486 PHE 0.008 0.001 PHE A 730 TYR 0.017 0.002 TYR A 986 ARG 0.009 0.000 ARG A1048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6670.65 seconds wall clock time: 116 minutes 47.82 seconds (7007.82 seconds total)