Starting phenix.real_space_refine on Sun Mar 10 14:59:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/03_2024/8edl_28035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/03_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_28035/03_2024/8edl_28035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/03_2024/8edl_28035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/03_2024/8edl_28035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edl_28035/03_2024/8edl_28035.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.97, per 1000 atoms: 0.80 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 - 3.50 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: 1.14 Conformation dependent library (CDL) restraints added in 547.7 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: 0.27 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: 0.75 Time building geometry restraints manager: 1.24 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: 94.56 - 102.43: 9 102.43 - 110.29: 542 110.29 - 118.16: 1346 118.16 - 126.03: 1492 126.03 - 133.90: 35 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 2.520 nonbonded pdb=" O LYS A 584 " pdb=" OG SER A 587 " model vdw 2.312 2.440 nonbonded pdb=" O TRP A 784 " pdb=" OG1 THR A 788 " model vdw 2.334 2.440 nonbonded pdb=" O PHE A 944 " pdb=" N LEU A 952 " model vdw 2.350 2.520 nonbonded pdb=" O LEU A 792 " pdb=" NE2 HIS A 906 " model vdw 2.476 2.520 ... (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: 0.910 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: 0.000 Extract box with map and model: 3.640 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.500 Find NCS groups from input model: 0.090 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- 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 : 0.279 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: 0.1744 time to fit residues: 13.8655 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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** A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2504 Z= 0.153 Angle : 0.497 7.433 3424 Z= 0.260 Chirality : 0.034 0.115 417 Planarity : 0.004 0.036 452 Dihedral : 3.314 14.936 406 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.35 % Favored : 97.39 % 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: 3.06 (0.44), residues: 383 helix: 2.67 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -0.50 (0.74), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 837 HIS 0.007 0.001 HIS A 781 PHE 0.008 0.002 PHE A 945 TYR 0.010 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 57 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 587 SER cc_start: 0.6990 (t) cc_final: 0.6782 (p) REVERT: A 794 TYR cc_start: 0.7242 (t80) cc_final: 0.7016 (t80) REVERT: A 957 ASN cc_start: 0.8165 (m-40) cc_final: 0.7818 (m-40) REVERT: A 985 GLN cc_start: 0.5089 (mp10) cc_final: 0.4238 (mm-40) REVERT: A 1041 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7065 (tpp) outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 0.1480 time to fit residues: 9.6894 Evaluate side-chains 46 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 904 CYS Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.0170 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4622 ------------------------------------------------------------------------------- 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: 0.7035 moved from start: 0.7392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2504 Z= 0.231 Angle : 0.548 6.611 3424 Z= 0.301 Chirality : 0.036 0.124 417 Planarity : 0.004 0.033 452 Dihedral : 3.615 17.171 406 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.13 % Favored : 96.61 % Rotamer: Outliers : 3.08 % Allowed : 16.92 % Favored : 80.00 % 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: 2.63 (0.43), residues: 383 helix: 2.39 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.70 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 599 HIS 0.004 0.001 HIS A 982 PHE 0.009 0.002 PHE A 945 TYR 0.012 0.002 TYR A 998 ARG 0.004 0.001 ARG A1000 *********************** 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 51 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 587 SER cc_start: 0.7587 (t) cc_final: 0.7242 (p) REVERT: A 594 THR cc_start: 0.8723 (p) cc_final: 0.8468 (p) REVERT: A 686 LYS cc_start: 0.8291 (tppt) cc_final: 0.7908 (mmmt) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1167 time to fit residues: 7.1701 Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 696 TRP Chi-restraints excluded: chain A residue 904 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** A 712 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.7726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2504 Z= 0.139 Angle : 0.455 5.325 3424 Z= 0.248 Chirality : 0.034 0.110 417 Planarity : 0.003 0.025 452 Dihedral : 3.305 14.732 406 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.54 % Allowed : 20.77 % Favored : 77.69 % 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: 3.13 (0.43), residues: 383 helix: 2.74 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.48 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 837 HIS 0.004 0.001 HIS A 982 PHE 0.013 0.002 PHE A 843 TYR 0.006 0.001 TYR A 998 ARG 0.002 0.001 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 : 0.305 Fit side-chains revert: symmetry clash REVERT: A 587 SER cc_start: 0.7814 (t) cc_final: 0.7496 (p) REVERT: A 686 LYS cc_start: 0.8242 (tppt) cc_final: 0.7952 (tppt) outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.1008 time to fit residues: 5.7698 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 904 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** A 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.8677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2504 Z= 0.171 Angle : 0.489 7.940 3424 Z= 0.263 Chirality : 0.035 0.122 417 Planarity : 0.003 0.027 452 Dihedral : 3.398 14.973 406 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.85 % Allowed : 20.00 % Favored : 76.15 % 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: 2.97 (0.43), residues: 383 helix: 2.63 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.61 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 777 HIS 0.001 0.001 HIS A 982 PHE 0.012 0.001 PHE A 843 TYR 0.019 0.002 TYR A 794 ARG 0.004 0.001 ARG A1038 *********************** 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 50 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 583 LYS cc_start: 0.8230 (mmtp) cc_final: 0.7939 (mmmt) REVERT: A 605 ILE cc_start: 0.8023 (pt) cc_final: 0.7698 (tt) REVERT: A 686 LYS cc_start: 0.8250 (tppt) cc_final: 0.8012 (tppt) REVERT: A 1041 MET cc_start: 0.8495 (tpp) cc_final: 0.8243 (mpp) outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 0.1222 time to fit residues: 6.9677 Evaluate side-chains 44 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 693 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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: 0.7095 moved from start: 0.9009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2504 Z= 0.141 Angle : 0.442 6.015 3424 Z= 0.238 Chirality : 0.034 0.108 417 Planarity : 0.002 0.023 452 Dihedral : 3.200 14.350 406 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.38 % Allowed : 17.69 % 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: 3.32 (0.43), residues: 383 helix: 2.85 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.35 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1048 HIS 0.001 0.000 HIS A 982 PHE 0.012 0.001 PHE A 843 TYR 0.012 0.001 TYR A 794 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 50 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 583 LYS cc_start: 0.8271 (mmtp) cc_final: 0.7949 (mmmt) REVERT: A 686 LYS cc_start: 0.8229 (tppt) cc_final: 0.7994 (tppt) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.1336 time to fit residues: 7.4158 Evaluate side-chains 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 904 CYS Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 993 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.7140 moved from start: 0.9467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2504 Z= 0.190 Angle : 0.513 5.427 3424 Z= 0.277 Chirality : 0.035 0.137 417 Planarity : 0.003 0.024 452 Dihedral : 3.478 14.584 406 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.85 % Allowed : 22.31 % 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: 2.95 (0.43), residues: 383 helix: 2.59 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -0.42 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1048 HIS 0.003 0.001 HIS A 906 PHE 0.016 0.002 PHE A1037 TYR 0.010 0.002 TYR A 998 ARG 0.006 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 49 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 583 LYS cc_start: 0.8266 (mmtp) cc_final: 0.7896 (mmmt) REVERT: A 686 LYS cc_start: 0.8263 (tppt) cc_final: 0.8033 (mmmm) REVERT: A 1041 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8048 (mpp) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.1207 time to fit residues: 6.7082 Evaluate side-chains 46 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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: 0.7087 moved from start: 0.9526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2504 Z= 0.127 Angle : 0.465 6.671 3424 Z= 0.249 Chirality : 0.034 0.140 417 Planarity : 0.002 0.021 452 Dihedral : 3.153 12.984 406 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.31 % Allowed : 23.08 % Favored : 74.62 % 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: 2.88 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.20 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1048 HIS 0.001 0.000 HIS A 781 PHE 0.019 0.002 PHE A1037 TYR 0.012 0.001 TYR A1044 ARG 0.002 0.000 ARG A1038 *********************** 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 48 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 583 LYS cc_start: 0.8313 (mmtp) cc_final: 0.7911 (mmmt) REVERT: A 605 ILE cc_start: 0.8154 (pt) cc_final: 0.7820 (tt) REVERT: A 686 LYS cc_start: 0.8216 (tppt) cc_final: 0.7994 (tppt) REVERT: A 1041 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7786 (mpp) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.1199 time to fit residues: 6.7095 Evaluate side-chains 43 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7092 moved from start: 0.9739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2504 Z= 0.135 Angle : 0.514 8.545 3424 Z= 0.263 Chirality : 0.034 0.140 417 Planarity : 0.002 0.021 452 Dihedral : 3.098 12.656 406 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.08 % Allowed : 19.23 % Favored : 77.69 % 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: 3.47 (0.44), residues: 383 helix: 2.93 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -0.16 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1048 HIS 0.001 0.000 HIS A 781 PHE 0.018 0.002 PHE A1037 TYR 0.015 0.002 TYR A 794 ARG 0.006 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 : 0.307 Fit side-chains revert: symmetry clash REVERT: A 583 LYS cc_start: 0.8297 (mmtp) cc_final: 0.7892 (mmmt) REVERT: A 605 ILE cc_start: 0.8177 (pt) cc_final: 0.7834 (tt) REVERT: A 686 LYS cc_start: 0.8228 (tppt) cc_final: 0.8008 (tppt) REVERT: A 1041 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7932 (mpp) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1224 time to fit residues: 6.4995 Evaluate side-chains 46 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 696 TRP Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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** A 684 GLN A 781 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.9862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2504 Z= 0.122 Angle : 0.496 7.751 3424 Z= 0.255 Chirality : 0.034 0.130 417 Planarity : 0.002 0.021 452 Dihedral : 2.970 12.131 406 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.31 % Allowed : 23.08 % Favored : 74.62 % 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: 3.71 (0.45), residues: 383 helix: 3.08 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.03 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1048 HIS 0.001 0.000 HIS A 781 PHE 0.020 0.002 PHE A1037 TYR 0.006 0.001 TYR A1044 ARG 0.002 0.000 ARG A 997 ********************** 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 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 583 LYS cc_start: 0.8341 (mmtp) cc_final: 0.7926 (mmmt) REVERT: A 605 ILE cc_start: 0.8180 (pt) cc_final: 0.7864 (tt) REVERT: A 1041 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7890 (mpp) outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.1209 time to fit residues: 6.7928 Evaluate side-chains 40 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1041 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.101613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.081495 restraints weight = 10011.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.082968 restraints weight = 7209.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.083648 restraints weight = 5838.020| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.9919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2504 Z= 0.123 Angle : 0.489 7.584 3424 Z= 0.253 Chirality : 0.034 0.126 417 Planarity : 0.002 0.022 452 Dihedral : 2.945 12.342 406 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.08 % Allowed : 23.08 % 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: 3.82 (0.45), residues: 383 helix: 3.16 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.05 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 837 HIS 0.001 0.000 HIS A 781 PHE 0.022 0.002 PHE A1037 TYR 0.005 0.001 TYR A 998 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: 865.06 seconds wall clock time: 16 minutes 8.60 seconds (968.60 seconds total)