Starting phenix.real_space_refine on Thu Feb 13 04:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2o_27144/02_2025/8d2o_27144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2o_27144/02_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_27144/02_2025/8d2o_27144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2o_27144/02_2025/8d2o_27144.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2o_27144/02_2025/8d2o_27144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2o_27144/02_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-5592/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: 5.03, per 1000 atoms: 0.59 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: 2.02 Conformation dependent library (CDL) restraints added in 680.8 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: 3.46 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: 4.22 Time building geometry restraints manager: 2.36 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: 1.840 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.490 Find NCS groups from input model: 0.080 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:15.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- 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 : 0.680 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: 1.7606 time to fit residues: 118.7706 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 : 0.785 ------------------------------------------------------------------------------- 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 = 0.181979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143475 restraints weight = 9005.591| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.34 r_work: 0.3402 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.728 Fit side-chains REVERT: A 116 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7243 (pt0) REVERT: A 125 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7110 (mtp180) REVERT: A 162 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6300 (mt-10) REVERT: A 1028 MET cc_start: 0.7505 (ptp) cc_final: 0.6842 (mmp) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 1.7524 time to fit residues: 108.7113 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 : 0.710 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 24 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.180887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141235 restraints weight = 9074.346| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.34 r_work: 0.3375 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1233 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= 0.172 Angle : 0.535 8.148 12655 Z= 0.283 Chirality : 0.037 0.223 1477 Planarity : 0.005 0.072 1187 Dihedral : 22.191 158.261 2597 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.98 % Allowed : 9.23 % 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: 1.63 (0.29), residues: 328 sheet: 0.00 (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 942 HIS 0.003 0.001 HIS A1100 PHE 0.005 0.001 PHE A 76 TYR 0.014 0.002 TYR A 698 ARG 0.010 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 60 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.801 Fit side-chains REVERT: A 125 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7090 (mtp180) REVERT: A 815 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 1028 MET cc_start: 0.7653 (ptp) cc_final: 0.6953 (mmp) outliers start: 12 outliers final: 4 residues processed: 57 average time/residue: 1.5521 time to fit residues: 93.6425 Evaluate side-chains 50 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 218 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 42 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.177608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138456 restraints weight = 9025.885| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.32 r_work: 0.3335 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8903 Z= 0.212 Angle : 0.553 8.544 12655 Z= 0.293 Chirality : 0.038 0.215 1477 Planarity : 0.005 0.083 1187 Dihedral : 22.167 156.455 2597 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.29 % Allowed : 9.72 % Favored : 86.99 % 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: 0.85 (0.30), residues: 739 helix: 1.78 (0.29), residues: 328 sheet: -0.04 (0.56), residues: 85 loop : -0.50 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 13 HIS 0.004 0.001 HIS A1100 PHE 0.006 0.001 PHE A 730 TYR 0.016 0.002 TYR A 986 ARG 0.008 0.000 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 69 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.775 Fit side-chains REVERT: A 14 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8090 (mtm-85) REVERT: A 125 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7091 (mtp180) REVERT: A 162 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6375 (mt-10) REVERT: A 684 THR cc_start: 0.5357 (OUTLIER) cc_final: 0.4982 (p) REVERT: A 815 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 1028 MET cc_start: 0.7666 (ptp) cc_final: 0.6934 (mmp) outliers start: 20 outliers final: 5 residues processed: 65 average time/residue: 1.6453 time to fit residues: 113.1229 Evaluate side-chains 57 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 684 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.178075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138091 restraints weight = 8972.887| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.34 r_work: 0.3342 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8903 Z= 0.195 Angle : 0.543 7.452 12655 Z= 0.286 Chirality : 0.038 0.223 1477 Planarity : 0.005 0.073 1187 Dihedral : 22.114 156.270 2597 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.98 % Allowed : 12.69 % Favored : 85.34 % 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: 0.96 (0.30), residues: 739 helix: 1.87 (0.29), residues: 328 sheet: -0.12 (0.55), residues: 85 loop : -0.38 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 721 HIS 0.003 0.001 HIS A1100 PHE 0.007 0.001 PHE A 730 TYR 0.015 0.002 TYR A 986 ARG 0.010 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 60 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.805 Fit side-chains REVERT: A 14 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8068 (mtm-85) REVERT: A 125 ARG cc_start: 0.7537 (mtp85) cc_final: 0.7052 (mtp180) REVERT: A 482 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: A 506 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8214 (mmm160) REVERT: A 684 THR cc_start: 0.5457 (OUTLIER) cc_final: 0.5066 (p) REVERT: A 692 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7288 (ttp80) REVERT: A 815 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 866 GLU cc_start: 0.7511 (mp0) cc_final: 0.7295 (mp0) REVERT: A 1028 MET cc_start: 0.7721 (ptp) cc_final: 0.6989 (mmp) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 1.6722 time to fit residues: 100.6603 Evaluate side-chains 56 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.174639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134075 restraints weight = 8932.155| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.37 r_work: 0.3267 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8903 Z= 0.338 Angle : 0.642 8.194 12655 Z= 0.336 Chirality : 0.043 0.228 1477 Planarity : 0.006 0.086 1187 Dihedral : 22.309 154.185 2597 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.13 % Allowed : 12.52 % 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 (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: 0.59 (0.30), residues: 739 helix: 1.49 (0.29), residues: 331 sheet: -0.35 (0.53), residues: 85 loop : -0.51 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 145 HIS 0.005 0.001 HIS A 936 PHE 0.009 0.002 PHE A 730 TYR 0.021 0.003 TYR A 986 ARG 0.009 0.001 ARG A1048 *********************** 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 68 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.767 Fit side-chains REVERT: A 14 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8009 (mtm-85) REVERT: A 125 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7059 (mtp180) REVERT: A 190 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7706 (mm110) REVERT: A 482 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: A 684 THR cc_start: 0.5294 (OUTLIER) cc_final: 0.4918 (p) REVERT: A 692 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7334 (ttp80) REVERT: A 815 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 904 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6697 (ptt-90) REVERT: A 1028 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6992 (mmp) outliers start: 19 outliers final: 9 residues processed: 61 average time/residue: 1.5035 time to fit residues: 97.4469 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 : 0.722 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.177741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138679 restraints weight = 9079.121| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.37 r_work: 0.3345 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1833 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= 0.185 Angle : 0.546 8.400 12655 Z= 0.290 Chirality : 0.038 0.232 1477 Planarity : 0.005 0.087 1187 Dihedral : 22.140 155.698 2597 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.98 % Allowed : 14.83 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.30), residues: 739 helix: 1.80 (0.29), residues: 328 sheet: -0.39 (0.54), residues: 85 loop : -0.40 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.003 0.001 HIS A 936 PHE 0.008 0.001 PHE A 730 TYR 0.014 0.002 TYR A 986 ARG 0.014 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 61 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.803 Fit side-chains REVERT: A 14 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8060 (mtm-85) REVERT: A 125 ARG cc_start: 0.7496 (mtp85) cc_final: 0.7015 (mtm180) REVERT: A 147 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7916 (p) REVERT: A 684 THR cc_start: 0.5411 (OUTLIER) cc_final: 0.5040 (p) REVERT: A 692 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7336 (ttp80) REVERT: A 815 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7671 (mp) REVERT: A 1028 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6988 (mmp) outliers start: 12 outliers final: 6 residues processed: 58 average time/residue: 1.6010 time to fit residues: 98.2020 Evaluate side-chains 58 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 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 7 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.175466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136424 restraints weight = 9137.368| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.40 r_work: 0.3304 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8903 Z= 0.333 Angle : 0.632 10.493 12655 Z= 0.331 Chirality : 0.043 0.227 1477 Planarity : 0.005 0.037 1187 Dihedral : 22.265 154.289 2597 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.97 % Allowed : 14.33 % 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 (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: 0.62 (0.30), residues: 739 helix: 1.60 (0.29), residues: 330 sheet: -0.51 (0.53), residues: 85 loop : -0.53 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 145 HIS 0.005 0.001 HIS A 936 PHE 0.008 0.001 PHE A 730 TYR 0.020 0.002 TYR A 986 ARG 0.009 0.001 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: 18 poor density : 47 time to evaluate : 0.812 Fit side-chains REVERT: A 14 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8071 (mtm-85) REVERT: A 125 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7056 (mtp180) REVERT: A 190 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7692 (mm110) REVERT: A 684 THR cc_start: 0.5556 (OUTLIER) cc_final: 0.5177 (p) REVERT: A 692 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7393 (ttp80) REVERT: A 815 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 1028 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7020 (mmp) REVERT: A 1048 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7981 (mmm-85) outliers start: 18 outliers final: 10 residues processed: 60 average time/residue: 1.4140 time to fit residues: 90.2583 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 : 0.782 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 chunk 68 optimal weight: 0.0010 chunk 25 optimal weight: 0.0040 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 overall best weight: 0.2598 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.183184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144622 restraints weight = 9218.409| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.47 r_work: 0.3431 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8903 Z= 0.147 Angle : 0.520 6.891 12655 Z= 0.277 Chirality : 0.037 0.250 1477 Planarity : 0.004 0.034 1187 Dihedral : 22.016 156.985 2597 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.48 % Allowed : 15.32 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.30), residues: 739 helix: 1.90 (0.29), residues: 329 sheet: -0.46 (0.54), residues: 85 loop : -0.29 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.003 0.001 HIS A 486 PHE 0.008 0.001 PHE A 730 TYR 0.014 0.002 TYR A 800 ARG 0.005 0.000 ARG A 911 *********************** 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 59 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.781 Fit side-chains REVERT: A 14 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8143 (mtm-85) REVERT: A 684 THR cc_start: 0.5554 (OUTLIER) cc_final: 0.5194 (p) REVERT: A 692 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7362 (ttp80) REVERT: A 866 GLU cc_start: 0.7473 (mp0) cc_final: 0.7240 (mp0) REVERT: A 1028 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7026 (mmp) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 1.7044 time to fit residues: 102.4332 Evaluate side-chains 58 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 849 THR 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: 0.9980 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.177791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137815 restraints weight = 8985.747| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.48 r_work: 0.3347 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8903 Z= 0.241 Angle : 0.569 7.142 12655 Z= 0.300 Chirality : 0.039 0.223 1477 Planarity : 0.005 0.037 1187 Dihedral : 22.152 155.466 2597 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.48 % Allowed : 15.65 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.30), residues: 739 helix: 1.85 (0.29), residues: 330 sheet: -0.44 (0.54), residues: 85 loop : -0.36 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.005 0.001 HIS A 936 PHE 0.007 0.001 PHE A 730 TYR 0.017 0.003 TYR A1123 ARG 0.009 0.000 ARG A 911 ********************** 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 58 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.777 Fit side-chains REVERT: A 14 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8068 (mtm-85) REVERT: A 150 ASP cc_start: 0.7876 (m-30) cc_final: 0.7014 (t0) REVERT: A 684 THR cc_start: 0.5672 (OUTLIER) cc_final: 0.5309 (p) REVERT: A 692 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7403 (ttp80) REVERT: A 866 GLU cc_start: 0.7567 (mp0) cc_final: 0.7275 (mp0) REVERT: A 1028 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6991 (mmp) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 1.6608 time to fit residues: 96.8317 Evaluate side-chains 57 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 849 THR 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: 3.9990 chunk 78 optimal weight: 5.9990 chunk 17 optimal weight: 0.0470 chunk 25 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138948 restraints weight = 9206.381| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.48 r_work: 0.3344 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1893 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= 0.196 Angle : 0.548 7.145 12655 Z= 0.290 Chirality : 0.038 0.227 1477 Planarity : 0.004 0.047 1187 Dihedral : 22.122 155.334 2597 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.48 % Allowed : 16.31 % 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: 0.93 (0.30), residues: 739 helix: 1.86 (0.29), residues: 330 sheet: -0.42 (0.54), residues: 85 loop : -0.34 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.003 0.001 HIS A1100 PHE 0.007 0.001 PHE A 730 TYR 0.019 0.002 TYR A1123 ARG 0.008 0.000 ARG A1048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6220.82 seconds wall clock time: 110 minutes 18.96 seconds (6618.96 seconds total)