Starting phenix.real_space_refine on Wed Feb 14 02:41:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2o_27144/02_2024/8d2o_27144.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2o_27144/02_2024/8d2o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2o_27144/02_2024/8d2o_27144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2o_27144/02_2024/8d2o_27144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2o_27144/02_2024/8d2o_27144.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2o_27144/02_2024/8d2o_27144.pdb" } 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 Residue "A ASP 224": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.61, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 4.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.83 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: 3.98 Time building geometry restraints manager: 4.54 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: 99.04 - 106.05: 853 106.05 - 113.07: 4813 113.07 - 120.08: 3260 120.08 - 127.09: 3346 127.09 - 134.10: 383 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 2.440 nonbonded pdb=" OG SER A 59 " pdb=" OP1 C B 17 " model vdw 2.306 2.440 nonbonded pdb=" O LEU A 842 " pdb=" O2' C B 26 " model vdw 2.320 2.440 nonbonded pdb=" O2' A B 40 " pdb=" O4' A B 41 " model vdw 2.321 2.440 ... (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 ========== 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: 1.330 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: 6.460 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 32.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.270 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.768 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: 1.6686 time to fit residues: 112.5497 Evaluate side-chains 42 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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: 3.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 77 optimal weight: 8.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8903 Z= 0.287 Angle : 0.610 6.385 12655 Z= 0.323 Chirality : 0.041 0.205 1477 Planarity : 0.006 0.086 1187 Dihedral : 22.371 159.337 2597 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.98 % Allowed : 7.41 % Favored : 90.61 % 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: -0.03 (0.29), residues: 739 helix: 0.93 (0.29), residues: 327 sheet: -0.05 (0.55), residues: 83 loop : -0.95 (0.28), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1128 HIS 0.005 0.001 HIS A 47 PHE 0.007 0.001 PHE A 730 TYR 0.020 0.002 TYR A 986 ARG 0.005 0.001 ARG A1048 *********************** 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 65 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.665 Fit side-chains REVERT: A 116 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: A 125 ARG cc_start: 0.7348 (mtp85) cc_final: 0.7001 (mtm180) REVERT: A 815 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 1028 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7083 (mmp) outliers start: 12 outliers final: 5 residues processed: 58 average time/residue: 1.6900 time to fit residues: 103.1373 Evaluate side-chains 51 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8903 Z= 0.275 Angle : 0.597 8.662 12655 Z= 0.315 Chirality : 0.041 0.209 1477 Planarity : 0.006 0.101 1187 Dihedral : 22.327 157.786 2597 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.13 % Allowed : 10.54 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.29), residues: 739 helix: 1.33 (0.29), residues: 329 sheet: -0.06 (0.55), residues: 83 loop : -0.78 (0.29), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 942 HIS 0.005 0.001 HIS A 936 PHE 0.008 0.001 PHE A 730 TYR 0.019 0.002 TYR A 986 ARG 0.015 0.001 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 68 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.817 Fit side-chains REVERT: A 14 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7879 (mtm-85) REVERT: A 116 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: A 125 ARG cc_start: 0.7434 (mtp85) cc_final: 0.6983 (mtp180) REVERT: A 815 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7970 (mp) REVERT: A 1028 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7081 (mmp) outliers start: 19 outliers final: 9 residues processed: 62 average time/residue: 1.5925 time to fit residues: 104.4711 Evaluate side-chains 59 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 903 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 7.9990 chunk 58 optimal weight: 0.0770 chunk 40 optimal weight: 0.0020 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 overall best weight: 0.3344 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8903 Z= 0.146 Angle : 0.503 6.597 12655 Z= 0.269 Chirality : 0.036 0.234 1477 Planarity : 0.004 0.042 1187 Dihedral : 22.072 158.803 2597 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.31 % Allowed : 12.36 % 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: 0.85 (0.30), residues: 739 helix: 1.79 (0.29), residues: 328 sheet: -0.10 (0.56), residues: 83 loop : -0.48 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.003 0.001 HIS A 486 PHE 0.006 0.001 PHE A 730 TYR 0.013 0.002 TYR A1123 ARG 0.005 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 fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.812 Fit side-chains REVERT: A 125 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6852 (mtm180) REVERT: A 147 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 684 THR cc_start: 0.5530 (OUTLIER) cc_final: 0.5235 (p) REVERT: A 815 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7901 (mp) REVERT: A 1028 MET cc_start: 0.7444 (ptp) cc_final: 0.7123 (mmp) outliers start: 14 outliers final: 3 residues processed: 67 average time/residue: 1.4879 time to fit residues: 105.5392 Evaluate side-chains 57 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 147 THR 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 1118 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8903 Z= 0.302 Angle : 0.604 6.979 12655 Z= 0.315 Chirality : 0.041 0.205 1477 Planarity : 0.005 0.072 1187 Dihedral : 22.260 155.976 2597 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.62 % Allowed : 13.51 % 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: 0.70 (0.30), residues: 739 helix: 1.63 (0.29), residues: 330 sheet: -0.27 (0.54), residues: 83 loop : -0.50 (0.30), residues: 326 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 0.009 0.001 PHE A 730 TYR 0.020 0.003 TYR A 986 ARG 0.010 0.001 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 72 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 0.850 Fit side-chains REVERT: A 14 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7870 (mtm-85) REVERT: A 125 ARG cc_start: 0.7411 (mtp85) cc_final: 0.6940 (mtp85) REVERT: A 482 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: A 506 ARG cc_start: 0.8540 (mmm160) cc_final: 0.8331 (mmm160) REVERT: A 684 THR cc_start: 0.5434 (OUTLIER) cc_final: 0.5116 (p) REVERT: A 815 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 1028 MET cc_start: 0.7530 (ptp) cc_final: 0.7089 (mmp) REVERT: A 1045 ASP cc_start: 0.8160 (p0) cc_final: 0.7905 (p0) outliers start: 22 outliers final: 9 residues processed: 66 average time/residue: 1.4270 time to fit residues: 99.8552 Evaluate side-chains 60 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 849 THR Chi-restraints excluded: chain A residue 900 VAL 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 73 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8903 Z= 0.292 Angle : 0.601 7.612 12655 Z= 0.316 Chirality : 0.041 0.209 1477 Planarity : 0.005 0.071 1187 Dihedral : 22.277 155.399 2597 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.62 % Allowed : 14.00 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.30), residues: 739 helix: 1.50 (0.29), residues: 330 sheet: -0.38 (0.54), residues: 83 loop : -0.55 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 13 HIS 0.005 0.001 HIS A 936 PHE 0.009 0.001 PHE A 730 TYR 0.019 0.003 TYR A 986 ARG 0.012 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 70 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.856 Fit side-chains REVERT: A 14 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7814 (mtm-85) REVERT: A 125 ARG cc_start: 0.7420 (mtp85) cc_final: 0.6965 (mtp180) REVERT: A 684 THR cc_start: 0.5382 (OUTLIER) cc_final: 0.5105 (p) REVERT: A 692 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7389 (ttp80) REVERT: A 815 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7958 (mp) REVERT: A 1028 MET cc_start: 0.7564 (ptp) cc_final: 0.7089 (mmp) REVERT: A 1045 ASP cc_start: 0.8100 (p0) cc_final: 0.7879 (p0) outliers start: 22 outliers final: 14 residues processed: 63 average time/residue: 1.3657 time to fit residues: 91.5442 Evaluate side-chains 62 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 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 11 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 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 822 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 904 ARG Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8903 Z= 0.315 Angle : 0.610 7.182 12655 Z= 0.321 Chirality : 0.042 0.209 1477 Planarity : 0.006 0.100 1187 Dihedral : 22.301 155.608 2597 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.46 % Allowed : 15.32 % Favored : 81.22 % 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: 0.49 (0.30), residues: 739 helix: 1.41 (0.29), residues: 331 sheet: -0.44 (0.54), residues: 83 loop : -0.55 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 854 HIS 0.005 0.001 HIS A 936 PHE 0.010 0.001 PHE A 730 TYR 0.020 0.003 TYR A 986 ARG 0.007 0.001 ARG A 137 *********************** 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 69 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 0.723 Fit side-chains REVERT: A 14 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7827 (mtm-85) REVERT: A 125 ARG cc_start: 0.7444 (mtp85) cc_final: 0.6982 (mtp180) REVERT: A 684 THR cc_start: 0.5557 (OUTLIER) cc_final: 0.5279 (p) REVERT: A 815 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 904 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6657 (ptt-90) REVERT: A 976 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7657 (mp0) outliers start: 21 outliers final: 14 residues processed: 63 average time/residue: 1.3631 time to fit residues: 91.2427 Evaluate side-chains 64 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 484 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 822 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 904 ARG Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL 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 48 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8903 Z= 0.207 Angle : 0.548 7.094 12655 Z= 0.290 Chirality : 0.038 0.215 1477 Planarity : 0.005 0.083 1187 Dihedral : 22.204 156.195 2597 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.80 % Allowed : 16.47 % Favored : 80.72 % 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: 0.74 (0.30), residues: 739 helix: 1.62 (0.29), residues: 330 sheet: -0.33 (0.55), residues: 83 loop : -0.41 (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 486 PHE 0.008 0.001 PHE A 730 TYR 0.019 0.002 TYR A1123 ARG 0.006 0.000 ARG A 692 *********************** 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 67 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.862 Fit side-chains REVERT: A 14 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7855 (mtm-85) REVERT: A 125 ARG cc_start: 0.7383 (mtp85) cc_final: 0.6916 (mtm180) REVERT: A 147 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 684 THR cc_start: 0.5627 (OUTLIER) cc_final: 0.5341 (p) REVERT: A 815 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 976 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: A 1028 MET cc_start: 0.7569 (ptt) cc_final: 0.7009 (mmp) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 1.4685 time to fit residues: 98.3009 Evaluate side-chains 63 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 822 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 A1060 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8903 Z= 0.220 Angle : 0.556 7.540 12655 Z= 0.293 Chirality : 0.039 0.215 1477 Planarity : 0.005 0.070 1187 Dihedral : 22.176 156.216 2597 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.80 % Allowed : 16.64 % Favored : 80.56 % 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: 0.79 (0.30), residues: 739 helix: 1.66 (0.29), residues: 330 sheet: -0.32 (0.55), residues: 83 loop : -0.37 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 141 HIS 0.004 0.001 HIS A 486 PHE 0.008 0.001 PHE A 730 TYR 0.021 0.002 TYR A1123 ARG 0.010 0.000 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 64 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 1.096 Fit side-chains REVERT: A 14 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7851 (mtm-85) REVERT: A 125 ARG cc_start: 0.7393 (mtp85) cc_final: 0.6926 (mtp180) REVERT: A 147 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7893 (p) REVERT: A 684 THR cc_start: 0.5646 (OUTLIER) cc_final: 0.5357 (p) REVERT: A 815 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 976 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: A 1028 MET cc_start: 0.7574 (ptt) cc_final: 0.7023 (mmp) REVERT: A 1064 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7386 (mp) outliers start: 17 outliers final: 10 residues processed: 60 average time/residue: 1.4405 time to fit residues: 92.0019 Evaluate side-chains 62 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 822 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1064 LEU 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 49 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1910 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= 0.159 Angle : 0.517 7.159 12655 Z= 0.275 Chirality : 0.037 0.226 1477 Planarity : 0.004 0.045 1187 Dihedral : 22.053 157.289 2597 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.31 % Allowed : 17.46 % Favored : 80.23 % 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: 1.01 (0.30), residues: 739 helix: 1.85 (0.29), residues: 329 sheet: -0.27 (0.56), residues: 83 loop : -0.25 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.004 0.001 HIS A 486 PHE 0.008 0.001 PHE A 730 TYR 0.015 0.002 TYR A1123 ARG 0.010 0.000 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 62 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.742 Fit side-chains REVERT: A 14 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7855 (mtm-85) REVERT: A 125 ARG cc_start: 0.7353 (mtp85) cc_final: 0.6879 (mtm180) REVERT: A 684 THR cc_start: 0.5745 (OUTLIER) cc_final: 0.5416 (p) REVERT: A 815 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7940 (mp) REVERT: A 976 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 1028 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6970 (mmp) REVERT: A 1064 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7350 (mp) outliers start: 14 outliers final: 7 residues processed: 58 average time/residue: 1.6417 time to fit residues: 100.5510 Evaluate side-chains 60 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 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 181 VAL 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 976 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1064 LEU 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 20 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.178418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138474 restraints weight = 9006.278| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.33 r_work: 0.3364 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8903 Z= 0.202 Angle : 0.531 7.027 12655 Z= 0.281 Chirality : 0.038 0.216 1477 Planarity : 0.004 0.037 1187 Dihedral : 22.095 156.578 2597 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.31 % Allowed : 17.79 % Favored : 79.90 % 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: 1.01 (0.30), residues: 739 helix: 1.87 (0.29), residues: 329 sheet: -0.29 (0.54), residues: 85 loop : -0.26 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 486 PHE 0.008 0.001 PHE A 730 TYR 0.022 0.002 TYR A1123 ARG 0.010 0.000 ARG A1048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.48 seconds wall clock time: 47 minutes 54.11 seconds (2874.11 seconds total)