Starting phenix.real_space_refine on Fri Dec 27 09:45:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiz_60610/12_2024/9iiz_60610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiz_60610/12_2024/9iiz_60610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iiz_60610/12_2024/9iiz_60610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiz_60610/12_2024/9iiz_60610.map" model { file = "/net/cci-nas-00/data/ceres_data/9iiz_60610/12_2024/9iiz_60610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiz_60610/12_2024/9iiz_60610.cif" } resolution = 3.8 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= 0.015 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 20 5.16 5 C 2414 2.51 5 N 708 2.21 5 O 889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4080 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3043 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 1 Chain: "B" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 22} Chain: "C" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 508 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna3p': 23} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.21, per 1000 atoms: 0.79 Number of scatterers: 4080 At special positions: 0 Unit cell: (66.4884, 83.6142, 100.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 49 15.00 O 889 8.00 N 708 7.00 C 2414 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: 1.01 Conformation dependent library (CDL) restraints added in 909.9 milliseconds 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 3 sheets defined 35.8% alpha, 13.3% beta 20 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 631 through 640 Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 645 through 650 removed outlier: 3.520A pdb=" N ILE A 649 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 692 through 704 removed outlier: 3.531A pdb=" N TYR A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 739 removed outlier: 4.041A pdb=" N VAL A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 819 removed outlier: 4.332A pdb=" N HIS A 801 " --> pdb=" O GLN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 removed outlier: 4.299A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 930 through 941 Processing helix chain 'A' and resid 955 through 971 removed outlier: 3.780A pdb=" N ASN A 959 " --> pdb=" O PRO A 955 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AA2, first strand: chain 'A' and resid 657 through 660 removed outlier: 6.411A pdb=" N ALA A 624 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 687 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 626 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 684 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 714 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE A 686 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 786 through 791 removed outlier: 4.120A pdb=" N ALA A 791 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA A 773 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL A 756 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 826 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 825 " --> pdb=" O ALA A 864 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 866 " --> pdb=" O ILE A 825 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 827 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 868 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 865 " --> pdb=" O ILE A 923 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.19 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: 1114 1.34 - 1.46: 1247 1.46 - 1.58: 1783 1.58 - 1.71: 96 1.71 - 1.83: 31 Bond restraints: 4271 Sorted by residual: bond pdb=" P G B 22 " pdb=" O5' G B 22 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.50e-02 4.44e+03 4.54e+00 bond pdb=" O5' G B 22 " pdb=" C5' G B 22 " ideal model delta sigma weight residual 1.420 1.451 -0.031 1.50e-02 4.44e+03 4.36e+00 bond pdb=" CB ASP A 982 " pdb=" CG ASP A 982 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.61e+00 bond pdb=" P G B 23 " pdb=" OP2 G B 23 " ideal model delta sigma weight residual 1.485 1.522 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" CA LYS A 739 " pdb=" C LYS A 739 " ideal model delta sigma weight residual 1.524 1.548 -0.025 1.38e-02 5.25e+03 3.21e+00 ... (remaining 4266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 5904 3.72 - 7.44: 84 7.44 - 11.17: 16 11.17 - 14.89: 4 14.89 - 18.61: 3 Bond angle restraints: 6011 Sorted by residual: angle pdb=" CA LYS A 739 " pdb=" CB LYS A 739 " pdb=" CG LYS A 739 " ideal model delta sigma weight residual 114.10 127.96 -13.86 2.00e+00 2.50e-01 4.81e+01 angle pdb=" CB MET A 736 " pdb=" CG MET A 736 " pdb=" SD MET A 736 " ideal model delta sigma weight residual 112.70 131.31 -18.61 3.00e+00 1.11e-01 3.85e+01 angle pdb=" CA MET A 736 " pdb=" CB MET A 736 " pdb=" CG MET A 736 " ideal model delta sigma weight residual 114.10 125.95 -11.85 2.00e+00 2.50e-01 3.51e+01 angle pdb=" C LEU A 984 " pdb=" N PHE A 985 " pdb=" CA PHE A 985 " ideal model delta sigma weight residual 120.38 128.07 -7.69 1.46e+00 4.69e-01 2.78e+01 angle pdb=" CA LEU A 967 " pdb=" CB LEU A 967 " pdb=" CG LEU A 967 " ideal model delta sigma weight residual 116.30 134.49 -18.19 3.50e+00 8.16e-02 2.70e+01 ... (remaining 6006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 2386 32.79 - 65.58: 225 65.58 - 98.37: 27 98.37 - 131.16: 2 131.16 - 163.95: 1 Dihedral angle restraints: 2641 sinusoidal: 1525 harmonic: 1116 Sorted by residual: dihedral pdb=" CA HIS A 943 " pdb=" C HIS A 943 " pdb=" N MET A 944 " pdb=" CA MET A 944 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" O4' U B 25 " pdb=" C1' U B 25 " pdb=" N1 U B 25 " pdb=" C2 U B 25 " ideal model delta sinusoidal sigma weight residual -128.00 -62.62 -65.38 1 1.70e+01 3.46e-03 1.94e+01 dihedral pdb=" O4' U B 1 " pdb=" C1' U B 1 " pdb=" N1 U B 1 " pdb=" C2 U B 1 " ideal model delta sinusoidal sigma weight residual -128.00 -70.13 -57.87 1 1.70e+01 3.46e-03 1.56e+01 ... (remaining 2638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 659 0.112 - 0.223: 46 0.223 - 0.335: 2 0.335 - 0.446: 1 0.446 - 0.558: 3 Chirality restraints: 711 Sorted by residual: chirality pdb=" P G B 22 " pdb=" OP1 G B 22 " pdb=" OP2 G B 22 " pdb=" O5' G B 22 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" P G B 23 " pdb=" OP1 G B 23 " pdb=" OP2 G B 23 " pdb=" O5' G B 23 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" P U B 25 " pdb=" OP1 U B 25 " pdb=" OP2 U B 25 " pdb=" O5' U B 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 708 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 646 " -0.043 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 647 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 647 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 647 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 647 " -0.042 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 648 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 678 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 679 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 679 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 679 " 0.032 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 913 2.79 - 3.31: 3616 3.31 - 3.84: 8013 3.84 - 4.37: 8518 4.37 - 4.90: 12876 Nonbonded interactions: 33936 Sorted by model distance: nonbonded pdb=" O LEU A 934 " pdb=" OG1 THR A 938 " model vdw 2.256 3.040 nonbonded pdb=" NE2 GLN A 793 " pdb=" O GLN A 795 " model vdw 2.291 3.120 nonbonded pdb=" NE2 GLN A 712 " pdb=" OE1 GLN A 735 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR A 954 " pdb=" OD1 ASN A 959 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASP A 760 " pdb=" OD2 ASP A 830 " model vdw 2.324 3.040 ... (remaining 33931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.210 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 16.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4271 Z= 0.335 Angle : 1.234 18.610 6011 Z= 0.595 Chirality : 0.068 0.558 711 Planarity : 0.007 0.064 585 Dihedral : 22.766 163.954 1917 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.59 % Allowed : 29.79 % Favored : 69.62 % 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: -3.44 (0.38), residues: 373 helix: -2.03 (0.41), residues: 118 sheet: -0.75 (0.64), residues: 72 loop : -3.17 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 745 HIS 0.004 0.001 HIS A 943 PHE 0.037 0.002 PHE A 986 TYR 0.024 0.002 TYR A 901 ARG 0.007 0.001 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 MET cc_start: -0.2981 (ptt) cc_final: -0.3284 (ptt) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.1974 time to fit residues: 16.3361 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 687 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4271 Z= 0.221 Angle : 0.802 11.799 6011 Z= 0.383 Chirality : 0.044 0.250 711 Planarity : 0.005 0.051 585 Dihedral : 22.957 157.477 1160 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.83 % Allowed : 27.43 % Favored : 68.73 % 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 (0.41), residues: 373 helix: -0.90 (0.45), residues: 116 sheet: -1.08 (0.62), residues: 78 loop : -2.73 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 786 HIS 0.005 0.001 HIS A 962 PHE 0.011 0.001 PHE A 985 TYR 0.007 0.001 TYR A 945 ARG 0.007 0.001 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5039 (tmm) cc_final: 0.4766 (tmm) REVERT: A 674 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6798 (ttm170) REVERT: A 748 GLU cc_start: 0.8286 (pp20) cc_final: 0.8054 (pp20) outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.2093 time to fit residues: 17.5785 Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 674 ARG Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 962 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4271 Z= 0.259 Angle : 0.833 12.605 6011 Z= 0.400 Chirality : 0.044 0.209 711 Planarity : 0.005 0.049 585 Dihedral : 22.871 160.398 1159 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.42 % Allowed : 28.91 % Favored : 66.67 % 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: -2.52 (0.41), residues: 373 helix: -0.58 (0.45), residues: 116 sheet: -1.42 (0.61), residues: 78 loop : -2.56 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 745 HIS 0.017 0.002 HIS A 962 PHE 0.011 0.002 PHE A 985 TYR 0.012 0.002 TYR A 945 ARG 0.006 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.5073 (tpt) cc_final: 0.4613 (tpt) REVERT: A 723 GLN cc_start: 0.8144 (pp30) cc_final: 0.7825 (pp30) REVERT: A 726 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7912 (tpp-160) outliers start: 15 outliers final: 10 residues processed: 76 average time/residue: 0.2065 time to fit residues: 18.9713 Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 987 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4271 Z= 0.207 Angle : 0.766 11.410 6011 Z= 0.367 Chirality : 0.043 0.188 711 Planarity : 0.005 0.048 585 Dihedral : 22.560 155.495 1159 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.42 % Allowed : 31.86 % Favored : 63.72 % 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: -2.33 (0.43), residues: 373 helix: -0.38 (0.47), residues: 116 sheet: -1.33 (0.60), residues: 80 loop : -2.48 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 786 HIS 0.003 0.001 HIS A 943 PHE 0.011 0.001 PHE A 985 TYR 0.012 0.001 TYR A 960 ARG 0.006 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4953 (tpt) cc_final: 0.4668 (tpt) REVERT: A 723 GLN cc_start: 0.8081 (pp30) cc_final: 0.7765 (pp30) REVERT: A 726 ARG cc_start: 0.8272 (mmt180) cc_final: 0.7970 (tpp-160) REVERT: A 844 GLU cc_start: 0.2796 (OUTLIER) cc_final: 0.2178 (mp0) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.1802 time to fit residues: 15.9283 Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 987 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4271 Z= 0.233 Angle : 0.780 11.360 6011 Z= 0.379 Chirality : 0.044 0.208 711 Planarity : 0.005 0.051 585 Dihedral : 22.575 157.532 1158 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.85 % Favored : 90.88 % Rotamer: Outliers : 6.19 % Allowed : 31.27 % Favored : 62.54 % 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: -2.20 (0.43), residues: 373 helix: 0.06 (0.49), residues: 109 sheet: -1.25 (0.61), residues: 80 loop : -2.57 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 745 HIS 0.004 0.001 HIS A 962 PHE 0.014 0.002 PHE A 985 TYR 0.011 0.002 TYR A 669 ARG 0.007 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.5269 (tpt) cc_final: 0.4967 (tpt) REVERT: A 683 MET cc_start: 0.0485 (ttt) cc_final: 0.0005 (ptm) REVERT: A 723 GLN cc_start: 0.8122 (pp30) cc_final: 0.7757 (pp30) REVERT: A 726 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7934 (tpp-160) REVERT: A 844 GLU cc_start: 0.2870 (OUTLIER) cc_final: 0.2235 (mp0) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 0.1831 time to fit residues: 17.2804 Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 987 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN A 818 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4271 Z= 0.200 Angle : 0.777 13.644 6011 Z= 0.369 Chirality : 0.044 0.226 711 Planarity : 0.005 0.059 585 Dihedral : 22.336 153.868 1158 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 5.60 % Allowed : 33.04 % Favored : 61.36 % 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: -2.08 (0.44), residues: 373 helix: 0.30 (0.51), residues: 107 sheet: -1.10 (0.63), residues: 78 loop : -2.60 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 PHE 0.012 0.001 PHE A 985 TYR 0.007 0.001 TYR A 669 ARG 0.011 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4955 (tpt) cc_final: 0.4685 (tpt) REVERT: A 683 MET cc_start: 0.0374 (ttt) cc_final: -0.0150 (ptm) REVERT: A 723 GLN cc_start: 0.8036 (pp30) cc_final: 0.7705 (pp30) REVERT: A 844 GLU cc_start: 0.2922 (OUTLIER) cc_final: 0.2350 (mp0) outliers start: 19 outliers final: 17 residues processed: 74 average time/residue: 0.1836 time to fit residues: 16.5290 Evaluate side-chains 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN A 818 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4271 Z= 0.188 Angle : 0.757 12.900 6011 Z= 0.365 Chirality : 0.044 0.200 711 Planarity : 0.005 0.060 585 Dihedral : 22.259 153.063 1158 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 5.31 % Allowed : 34.22 % Favored : 60.47 % 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: -2.05 (0.44), residues: 373 helix: 0.31 (0.52), residues: 108 sheet: -0.97 (0.65), residues: 77 loop : -2.63 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 PHE 0.011 0.001 PHE A 985 TYR 0.014 0.001 TYR A 669 ARG 0.010 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8883 (tppp) cc_final: 0.8676 (tppt) REVERT: A 723 GLN cc_start: 0.7990 (pp30) cc_final: 0.7703 (pp30) REVERT: A 844 GLU cc_start: 0.3070 (OUTLIER) cc_final: 0.2445 (mp0) outliers start: 18 outliers final: 16 residues processed: 72 average time/residue: 0.1521 time to fit residues: 14.0240 Evaluate side-chains 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN A 818 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4271 Z= 0.193 Angle : 0.765 14.093 6011 Z= 0.367 Chirality : 0.044 0.212 711 Planarity : 0.005 0.061 585 Dihedral : 22.203 152.085 1158 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.38 % Favored : 90.35 % Rotamer: Outliers : 6.49 % Allowed : 33.92 % Favored : 59.59 % 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: -2.06 (0.44), residues: 373 helix: 0.28 (0.51), residues: 109 sheet: -0.96 (0.63), residues: 77 loop : -2.65 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 745 HIS 0.003 0.000 HIS A 943 PHE 0.010 0.001 PHE A 985 TYR 0.016 0.002 TYR A 669 ARG 0.010 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8831 (tppp) cc_final: 0.8598 (tppt) REVERT: A 620 LEU cc_start: 0.6782 (mp) cc_final: 0.6535 (mp) REVERT: A 683 MET cc_start: -0.0066 (ttt) cc_final: -0.0344 (ptm) REVERT: A 723 GLN cc_start: 0.7984 (pp30) cc_final: 0.7687 (pp30) REVERT: A 844 GLU cc_start: 0.3021 (OUTLIER) cc_final: 0.2371 (mp0) outliers start: 22 outliers final: 19 residues processed: 76 average time/residue: 0.1803 time to fit residues: 17.0687 Evaluate side-chains 79 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4271 Z= 0.182 Angle : 0.789 15.303 6011 Z= 0.374 Chirality : 0.044 0.200 711 Planarity : 0.005 0.048 585 Dihedral : 22.118 151.154 1158 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.31 % Favored : 91.42 % Rotamer: Outliers : 4.13 % Allowed : 36.58 % Favored : 59.29 % 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: -2.13 (0.43), residues: 373 helix: 0.26 (0.51), residues: 109 sheet: -1.05 (0.63), residues: 77 loop : -2.69 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 745 HIS 0.002 0.000 HIS A 943 PHE 0.012 0.001 PHE A 852 TYR 0.019 0.002 TYR A 919 ARG 0.008 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLN cc_start: 0.7976 (pp30) cc_final: 0.7738 (pp30) REVERT: A 844 GLU cc_start: 0.2999 (OUTLIER) cc_final: 0.2353 (mp0) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.1691 time to fit residues: 15.2733 Evaluate side-chains 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4271 Z= 0.188 Angle : 0.802 15.277 6011 Z= 0.378 Chirality : 0.044 0.208 711 Planarity : 0.004 0.048 585 Dihedral : 22.071 150.874 1158 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.85 % Favored : 90.88 % Rotamer: Outliers : 4.13 % Allowed : 37.76 % Favored : 58.11 % 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: -2.15 (0.44), residues: 373 helix: 0.15 (0.50), residues: 115 sheet: -1.00 (0.63), residues: 77 loop : -2.76 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 745 HIS 0.002 0.000 HIS A 943 PHE 0.010 0.001 PHE A 852 TYR 0.019 0.002 TYR A 919 ARG 0.002 0.000 ARG A 921 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4980 (tpt) cc_final: 0.4706 (tpt) REVERT: A 723 GLN cc_start: 0.7971 (pp30) cc_final: 0.7722 (pp30) REVERT: A 921 ARG cc_start: 0.8294 (tpm170) cc_final: 0.7953 (ptm160) outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.1608 time to fit residues: 14.0511 Evaluate side-chains 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.175649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.153908 restraints weight = 12053.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.158812 restraints weight = 7555.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.162240 restraints weight = 5220.162| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4271 Z= 0.221 Angle : 0.817 15.268 6011 Z= 0.390 Chirality : 0.045 0.198 711 Planarity : 0.004 0.048 585 Dihedral : 22.216 152.570 1158 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.12 % Favored : 90.62 % Rotamer: Outliers : 4.72 % Allowed : 36.87 % Favored : 58.41 % 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: -2.17 (0.44), residues: 373 helix: 0.09 (0.50), residues: 116 sheet: -1.02 (0.63), residues: 77 loop : -2.75 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 PHE 0.016 0.002 PHE A 985 TYR 0.018 0.002 TYR A 919 ARG 0.002 0.000 ARG A 921 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.82 seconds wall clock time: 22 minutes 6.55 seconds (1326.55 seconds total)