Starting phenix.real_space_refine on Mon Sep 23 12:32:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/09_2024/8edl_28035.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/09_2024/8edl_28035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/09_2024/8edl_28035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/09_2024/8edl_28035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/09_2024/8edl_28035.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/09_2024/8edl_28035.cif" } resolution = 3.7 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= 0.002 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1552 2.51 5 N 469 2.21 5 O 434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2470 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2470 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PTRANS': 11, 'TRANS': 383} Chain breaks: 5 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 674 Unresolved non-hydrogen angles: 856 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 16, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 317 Time building chain proxies: 2.38, per 1000 atoms: 0.96 Number of scatterers: 2470 At special positions: 0 Unit cell: (94.64, 79.04, 66.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 434 8.00 N 469 7.00 C 1552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 475.9 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 592 through 618 Processing helix chain 'A' and resid 678 through 697 removed outlier: 3.884A pdb=" N TRP A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 721 removed outlier: 4.479A pdb=" N LEU A 704 " --> pdb=" O THR A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 734 through 747 removed outlier: 3.572A pdb=" N ALA A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 743 " --> pdb=" O MET A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 766 Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.538A pdb=" N LEU A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 792 " --> pdb=" O THR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 857 removed outlier: 4.611A pdb=" N GLY A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 902 removed outlier: 3.788A pdb=" N MET A 895 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 924 Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 929 through 943 removed outlier: 3.515A pdb=" N LYS A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 974 Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 988 through 1001 removed outlier: 4.023A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1024 Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 3.663A pdb=" N PHE A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.610A pdb=" N ALA A1081 " --> pdb=" O VAL A1077 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 864 1.34 - 1.46: 462 1.46 - 1.58: 1154 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 2504 Sorted by residual: bond pdb=" N GLN A 963 " pdb=" CA GLN A 963 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 3.79e+00 bond pdb=" C GLU A 962 " pdb=" N GLN A 963 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.31e-02 5.83e+03 2.56e+00 bond pdb=" CG MET A1041 " pdb=" SD MET A1041 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CA GLY A 751 " pdb=" C GLY A 751 " ideal model delta sigma weight residual 1.518 1.508 0.010 1.02e-02 9.61e+03 1.01e+00 bond pdb=" C GLY A 751 " pdb=" O GLY A 751 " ideal model delta sigma weight residual 1.230 1.236 -0.006 9.40e-03 1.13e+04 4.76e-01 ... (remaining 2499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 3322 1.27 - 2.54: 84 2.54 - 3.80: 11 3.80 - 5.07: 4 5.07 - 6.34: 3 Bond angle restraints: 3424 Sorted by residual: angle pdb=" CG MET A1041 " pdb=" SD MET A1041 " pdb=" CE MET A1041 " ideal model delta sigma weight residual 100.90 94.56 6.34 2.20e+00 2.07e-01 8.31e+00 angle pdb=" C LYS A 908 " pdb=" N VAL A 909 " pdb=" CA VAL A 909 " ideal model delta sigma weight residual 121.97 126.66 -4.69 1.80e+00 3.09e-01 6.79e+00 angle pdb=" CA MET A 992 " pdb=" CB MET A 992 " pdb=" CG MET A 992 " ideal model delta sigma weight residual 114.10 118.89 -4.79 2.00e+00 2.50e-01 5.74e+00 angle pdb=" CA VAL A 903 " pdb=" CB VAL A 903 " pdb=" CG1 VAL A 903 " ideal model delta sigma weight residual 110.40 114.25 -3.85 1.70e+00 3.46e-01 5.12e+00 angle pdb=" C LYS A1040 " pdb=" N MET A1041 " pdb=" CA MET A1041 " ideal model delta sigma weight residual 120.31 117.07 3.24 1.52e+00 4.33e-01 4.54e+00 ... (remaining 3419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.97: 1322 10.97 - 21.94: 93 21.94 - 32.91: 34 32.91 - 43.88: 17 43.88 - 54.85: 2 Dihedral angle restraints: 1468 sinusoidal: 316 harmonic: 1152 Sorted by residual: dihedral pdb=" CA LEU A1079 " pdb=" C LEU A1079 " pdb=" N LEU A1080 " pdb=" CA LEU A1080 " ideal model delta harmonic sigma weight residual -180.00 -165.38 -14.62 0 5.00e+00 4.00e-02 8.55e+00 dihedral pdb=" CA PHE A 894 " pdb=" CB PHE A 894 " pdb=" CG PHE A 894 " pdb=" CD1 PHE A 894 " ideal model delta sinusoidal sigma weight residual -20.00 34.85 -54.85 2 2.00e+01 2.50e-03 8.02e+00 dihedral pdb=" CA LEU A 933 " pdb=" CB LEU A 933 " pdb=" CG LEU A 933 " pdb=" CD1 LEU A 933 " ideal model delta sinusoidal sigma weight residual 180.00 136.02 43.98 3 1.50e+01 4.44e-03 7.91e+00 ... (remaining 1465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 268 0.027 - 0.054: 100 0.054 - 0.081: 38 0.081 - 0.108: 10 0.108 - 0.135: 1 Chirality restraints: 417 Sorted by residual: chirality pdb=" CA MET A1041 " pdb=" N MET A1041 " pdb=" C MET A1041 " pdb=" CB MET A1041 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA PRO A 733 " pdb=" N PRO A 733 " pdb=" C PRO A 733 " pdb=" CB PRO A 733 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.79e-01 chirality pdb=" CA ILE A 766 " pdb=" N ILE A 766 " pdb=" C ILE A 766 " pdb=" CB ILE A 766 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.51e-01 ... (remaining 414 not shown) Planarity restraints: 452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 962 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C GLU A 962 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU A 962 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 963 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1037 " -0.014 2.00e-02 2.50e+03 1.27e-02 2.83e+00 pdb=" CG PHE A1037 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A1037 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A1037 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A1037 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1037 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1037 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 889 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 890 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 890 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 890 " 0.020 5.00e-02 4.00e+02 ... (remaining 449 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 782 2.83 - 3.34: 2562 3.34 - 3.86: 3964 3.86 - 4.38: 4031 4.38 - 4.90: 6826 Nonbonded interactions: 18165 Sorted by model distance: nonbonded pdb=" O LEU A 952 " pdb=" ND2 ASN A 957 " model vdw 2.307 3.120 nonbonded pdb=" O LYS A 584 " pdb=" OG SER A 587 " model vdw 2.312 3.040 nonbonded pdb=" O TRP A 784 " pdb=" OG1 THR A 788 " model vdw 2.334 3.040 nonbonded pdb=" O PHE A 944 " pdb=" N LEU A 952 " model vdw 2.350 3.120 nonbonded pdb=" O LEU A 792 " pdb=" NE2 HIS A 906 " model vdw 2.476 3.120 ... (remaining 18160 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 group one per residue 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: 0.950 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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 : 0.002 0.027 2504 Z= 0.141 Angle : 0.520 6.341 3424 Z= 0.313 Chirality : 0.033 0.135 417 Planarity : 0.003 0.035 452 Dihedral : 11.073 54.855 710 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.09 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.83 (0.45), residues: 383 helix: 2.73 (0.30), residues: 275 sheet: None (None), residues: 0 loop : -0.45 (0.69), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 696 HIS 0.001 0.001 HIS A 906 PHE 0.029 0.002 PHE A1037 TYR 0.005 0.001 TYR A1044 ARG 0.002 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 1037 PHE cc_start: 0.7781 (t80) cc_final: 0.7534 (t80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1737 time to fit residues: 13.7569 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN A 712 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2504 Z= 0.160 Angle : 0.513 7.241 3424 Z= 0.267 Chirality : 0.035 0.129 417 Planarity : 0.004 0.039 452 Dihedral : 3.362 15.098 406 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.61 % Favored : 97.13 % Rotamer: Outliers : 3.85 % Allowed : 13.08 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.02 (0.44), residues: 383 helix: 2.63 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -0.44 (0.75), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 837 HIS 0.006 0.001 HIS A 781 PHE 0.007 0.002 PHE A 945 TYR 0.011 0.002 TYR A 998 ARG 0.004 0.001 ARG A1038 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 587 SER cc_start: 0.7329 (OUTLIER) cc_final: 0.7059 (p) REVERT: A 985 GLN cc_start: 0.5182 (mp10) cc_final: 0.4362 (mm-40) REVERT: A 1041 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7116 (tpp) outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 0.1428 time to fit residues: 9.1164 Evaluate side-chains 44 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 904 CYS Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2504 Z= 0.160 Angle : 0.485 6.813 3424 Z= 0.255 Chirality : 0.034 0.106 417 Planarity : 0.003 0.027 452 Dihedral : 3.038 14.956 406 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.69 % Rotamer: Outliers : 3.08 % Allowed : 15.38 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.40 (0.44), residues: 383 helix: 2.90 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -0.33 (0.73), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 777 HIS 0.003 0.001 HIS A 982 PHE 0.015 0.002 PHE A 843 TYR 0.014 0.002 TYR A 794 ARG 0.004 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 594 THR cc_start: 0.8578 (p) cc_final: 0.8290 (p) REVERT: A 686 LYS cc_start: 0.8340 (tppt) cc_final: 0.8085 (tppt) REVERT: A 985 GLN cc_start: 0.5206 (mp10) cc_final: 0.4421 (mm-40) REVERT: A 1041 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7428 (mpp) outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 0.0989 time to fit residues: 5.8057 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 904 CYS Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2504 Z= 0.125 Angle : 0.431 3.949 3424 Z= 0.228 Chirality : 0.034 0.109 417 Planarity : 0.003 0.024 452 Dihedral : 3.002 13.947 406 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.54 % Allowed : 21.54 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.62 (0.44), residues: 383 helix: 3.08 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.32 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 777 HIS 0.001 0.000 HIS A 982 PHE 0.014 0.001 PHE A 843 TYR 0.010 0.001 TYR A 794 ARG 0.003 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 686 LYS cc_start: 0.8347 (tppt) cc_final: 0.8139 (tppt) REVERT: A 985 GLN cc_start: 0.5472 (mp10) cc_final: 0.4653 (mm-40) REVERT: A 1041 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7699 (tpp) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.1013 time to fit residues: 5.8009 Evaluate side-chains 42 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2504 Z= 0.126 Angle : 0.409 5.990 3424 Z= 0.221 Chirality : 0.033 0.106 417 Planarity : 0.003 0.024 452 Dihedral : 2.953 13.791 406 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.31 % Allowed : 22.31 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.66 (0.44), residues: 383 helix: 3.08 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.18 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 777 HIS 0.001 0.000 HIS A 781 PHE 0.011 0.001 PHE A 843 TYR 0.006 0.001 TYR A 692 ARG 0.003 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 594 THR cc_start: 0.8780 (p) cc_final: 0.8580 (p) REVERT: A 938 LYS cc_start: 0.8035 (mttt) cc_final: 0.7769 (mttp) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.1243 time to fit residues: 7.2437 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 904 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2504 Z= 0.138 Angle : 0.435 5.816 3424 Z= 0.237 Chirality : 0.034 0.108 417 Planarity : 0.003 0.036 452 Dihedral : 3.060 13.997 406 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.31 % Allowed : 22.31 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.58 (0.44), residues: 383 helix: 3.01 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -0.09 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 777 HIS 0.001 0.000 HIS A 906 PHE 0.011 0.001 PHE A 843 TYR 0.007 0.001 TYR A 998 ARG 0.002 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 0.1436 time to fit residues: 7.7807 Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 693 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.9705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2504 Z= 0.368 Angle : 0.665 8.890 3424 Z= 0.366 Chirality : 0.040 0.145 417 Planarity : 0.004 0.039 452 Dihedral : 4.327 15.995 406 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.62 % Allowed : 20.00 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.76 (0.42), residues: 383 helix: 1.82 (0.28), residues: 295 sheet: None (None), residues: 0 loop : -1.07 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 837 HIS 0.002 0.001 HIS A 906 PHE 0.016 0.003 PHE A 710 TYR 0.018 0.003 TYR A 998 ARG 0.007 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.290 Fit side-chains REVERT: A 583 LYS cc_start: 0.8281 (mmtp) cc_final: 0.7924 (mmmt) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.1525 time to fit residues: 8.9087 Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 791 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.9746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2504 Z= 0.137 Angle : 0.470 7.218 3424 Z= 0.252 Chirality : 0.033 0.112 417 Planarity : 0.003 0.035 452 Dihedral : 3.373 13.219 406 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.77 % Allowed : 25.38 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.92 (0.43), residues: 383 helix: 2.57 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.50 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1048 HIS 0.001 0.000 HIS A 906 PHE 0.012 0.001 PHE A 843 TYR 0.007 0.001 TYR A1044 ARG 0.005 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.303 Fit side-chains REVERT: A 792 LEU cc_start: 0.8728 (mm) cc_final: 0.8245 (tp) REVERT: A 893 LYS cc_start: 0.6408 (mmtt) cc_final: 0.5861 (mptt) REVERT: A 1041 MET cc_start: 0.8514 (mmm) cc_final: 0.8079 (mpp) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1113 time to fit residues: 6.2258 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 1.0055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2504 Z= 0.205 Angle : 0.554 6.899 3424 Z= 0.294 Chirality : 0.036 0.108 417 Planarity : 0.004 0.036 452 Dihedral : 3.577 14.079 406 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.08 % Allowed : 24.62 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.67 (0.44), residues: 383 helix: 2.42 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.68 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1048 HIS 0.002 0.001 HIS A 906 PHE 0.011 0.002 PHE A 843 TYR 0.013 0.002 TYR A 998 ARG 0.005 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.298 Fit side-chains REVERT: A 1041 MET cc_start: 0.8578 (mmm) cc_final: 0.8060 (mpp) outliers start: 4 outliers final: 4 residues processed: 43 average time/residue: 0.1097 time to fit residues: 6.0074 Evaluate side-chains 42 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 696 TRP Chi-restraints excluded: chain A residue 791 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0170 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 0.0370 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 793 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 1.0067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 2504 Z= 0.131 Angle : 0.512 8.123 3424 Z= 0.265 Chirality : 0.034 0.111 417 Planarity : 0.003 0.035 452 Dihedral : 3.213 12.934 406 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.31 % Allowed : 25.38 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.15 (0.44), residues: 383 helix: 2.72 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.38 (0.76), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1048 HIS 0.001 0.000 HIS A 906 PHE 0.011 0.001 PHE A 843 TYR 0.009 0.001 TYR A1044 ARG 0.002 0.000 ARG A1000 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.284 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 42 average time/residue: 0.1160 time to fit residues: 6.2146 Evaluate side-chains 44 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 791 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** 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 = 0.3991 r_free = 0.3991 target = 0.099901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.079977 restraints weight = 9919.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.081264 restraints weight = 7314.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.082106 restraints weight = 5835.955| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 1.0166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 2504 Z= 0.136 Angle : 0.512 7.925 3424 Z= 0.265 Chirality : 0.034 0.110 417 Planarity : 0.003 0.034 452 Dihedral : 3.113 12.801 406 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 25.38 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.49 (0.45), residues: 383 helix: 2.94 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.20 (0.78), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1048 HIS 0.001 0.000 HIS A 906 PHE 0.011 0.001 PHE A 843 TYR 0.011 0.001 TYR A1044 ARG 0.002 0.000 ARG A 997 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 842.55 seconds wall clock time: 15 minutes 33.99 seconds (933.99 seconds total)