Starting phenix.real_space_refine on Tue Feb 11 03:40:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiz_60610/02_2025/9iiz_60610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiz_60610/02_2025/9iiz_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_60610/02_2025/9iiz_60610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiz_60610/02_2025/9iiz_60610.map" model { file = "/net/cci-nas-00/data/ceres_data/9iiz_60610/02_2025/9iiz_60610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiz_60610/02_2025/9iiz_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-5592/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: 3.14, per 1000 atoms: 0.77 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: 2.23 Conformation dependent library (CDL) restraints added in 977.1 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: 1.59 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: 1.46 Time building geometry restraints manager: 1.12 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: 0.260 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- 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 : 0.363 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: 0.2082 time to fit residues: 16.9951 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 : 0.315 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.178046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.155938 restraints weight = 11731.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.160933 restraints weight = 7319.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.164326 restraints weight = 5054.365| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5045 (tmm) cc_final: 0.4775 (tmm) REVERT: A 674 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6538 (ttm170) REVERT: A 748 GLU cc_start: 0.8323 (pp20) cc_final: 0.8086 (pp20) outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.2086 time to fit residues: 17.5596 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 : 0.427 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 40 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.177709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.156265 restraints weight = 11781.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.161020 restraints weight = 7522.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.164439 restraints weight = 5259.192| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4271 Z= 0.211 Angle : 0.789 12.484 6011 Z= 0.376 Chirality : 0.043 0.198 711 Planarity : 0.005 0.047 585 Dihedral : 22.661 158.119 1159 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.13 % Allowed : 29.20 % 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: -2.42 (0.42), residues: 373 helix: -0.45 (0.46), residues: 116 sheet: -1.25 (0.61), residues: 78 loop : -2.59 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.012 0.001 HIS A 962 PHE 0.010 0.001 PHE A 985 TYR 0.011 0.001 TYR A 669 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 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4794 (tpt) cc_final: 0.4290 (tpt) REVERT: A 674 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6306 (ttm170) REVERT: A 726 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7904 (tpp-160) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.2012 time to fit residues: 17.5289 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 : 0.336 ------------------------------------------------------------------------------- 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 674 ARG 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 915 VAL Chi-restraints excluded: chain A residue 962 HIS 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 27 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.180392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.159057 restraints weight = 11855.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.163849 restraints weight = 7506.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.167257 restraints weight = 5216.681| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.2432 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= 0.171 Angle : 0.740 11.586 6011 Z= 0.353 Chirality : 0.043 0.188 711 Planarity : 0.005 0.046 585 Dihedral : 22.375 153.671 1159 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.54 % Allowed : 30.68 % Favored : 65.78 % 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: -2.29 (0.43), residues: 373 helix: -0.26 (0.47), residues: 116 sheet: -1.17 (0.61), residues: 77 loop : -2.58 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 745 HIS 0.009 0.001 HIS A 962 PHE 0.009 0.001 PHE A 985 TYR 0.007 0.001 TYR A 669 ARG 0.006 0.000 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: 12 poor density : 63 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4600 (tpt) cc_final: 0.4079 (tpt) REVERT: A 674 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6607 (ttm170) REVERT: A 726 ARG cc_start: 0.8232 (mmt180) cc_final: 0.7894 (tpp-160) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.1879 time to fit residues: 16.4453 Evaluate side-chains 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 674 ARG Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 962 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 12 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.167114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.145111 restraints weight = 12575.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.149835 restraints weight = 7899.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.153144 restraints weight = 5520.572| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4271 Z= 0.380 Angle : 0.920 12.925 6011 Z= 0.454 Chirality : 0.048 0.238 711 Planarity : 0.006 0.055 585 Dihedral : 23.110 162.554 1158 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.19 % Favored : 89.54 % Rotamer: Outliers : 5.90 % Allowed : 30.97 % Favored : 63.13 % 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: -2.50 (0.42), residues: 373 helix: -0.28 (0.48), residues: 108 sheet: -1.60 (0.61), residues: 80 loop : -2.58 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 623 HIS 0.021 0.002 HIS A 962 PHE 0.016 0.002 PHE A 985 TYR 0.020 0.002 TYR A 960 ARG 0.008 0.001 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 83 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 673 LEU cc_start: 0.7487 (mt) cc_final: 0.7219 (mt) REVERT: A 730 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: A 844 GLU cc_start: 0.2717 (OUTLIER) cc_final: 0.2185 (mp0) REVERT: A 852 PHE cc_start: 0.7059 (m-80) cc_final: 0.6813 (m-80) outliers start: 20 outliers final: 13 residues processed: 78 average time/residue: 0.1890 time to fit residues: 18.0182 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 : 0.374 ------------------------------------------------------------------------------- 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 682 GLN 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 790 THR 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 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 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.177688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.155988 restraints weight = 12175.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.160612 restraints weight = 7892.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.164025 restraints weight = 5571.311| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4271 Z= 0.198 Angle : 0.776 13.621 6011 Z= 0.370 Chirality : 0.044 0.194 711 Planarity : 0.005 0.050 585 Dihedral : 22.299 152.141 1158 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.83 % Allowed : 34.81 % 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: -2.07 (0.44), residues: 373 helix: 0.17 (0.50), residues: 109 sheet: -1.11 (0.63), residues: 80 loop : -2.53 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 745 HIS 0.002 0.000 HIS A 943 PHE 0.014 0.001 PHE A 985 TYR 0.026 0.002 TYR A 669 ARG 0.009 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 77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.4720 (ppp) cc_final: 0.4462 (ppp) REVERT: A 651 MET cc_start: 0.4043 (tpt) cc_final: 0.3696 (tpt) REVERT: A 683 MET cc_start: -0.0284 (ttt) cc_final: -0.0619 (ptm) REVERT: A 723 GLN cc_start: 0.8163 (pp30) cc_final: 0.7940 (pp30) REVERT: A 921 ARG cc_start: 0.8290 (tpm170) cc_final: 0.8063 (ptp-170) outliers start: 13 outliers final: 12 residues processed: 73 average time/residue: 0.1851 time to fit residues: 16.4485 Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 790 THR Chi-restraints excluded: chain A residue 818 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.0370 overall best weight: 1.3462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.174902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153185 restraints weight = 12532.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.158019 restraints weight = 7939.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.161377 restraints weight = 5532.954| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4271 Z= 0.206 Angle : 0.768 13.247 6011 Z= 0.371 Chirality : 0.044 0.190 711 Planarity : 0.005 0.050 585 Dihedral : 22.387 154.670 1158 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.13 % Allowed : 35.40 % 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: -2.12 (0.44), residues: 373 helix: 0.12 (0.49), residues: 109 sheet: -1.06 (0.63), residues: 80 loop : -2.58 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 PHE 0.011 0.002 PHE A 985 TYR 0.026 0.002 TYR A 669 ARG 0.007 0.000 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 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8957 (tppp) cc_final: 0.8712 (tppt) REVERT: A 601 MET cc_start: 0.4885 (ppp) cc_final: 0.4626 (ppp) REVERT: A 651 MET cc_start: 0.4449 (tpt) cc_final: 0.4182 (tpt) REVERT: A 683 MET cc_start: 0.0063 (ttt) cc_final: -0.0309 (ptm) outliers start: 14 outliers final: 12 residues processed: 72 average time/residue: 0.1625 time to fit residues: 14.7390 Evaluate side-chains 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4342 r_free = 0.4342 target = 0.165008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.142832 restraints weight = 12380.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.147300 restraints weight = 7915.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.150480 restraints weight = 5564.994| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4271 Z= 0.392 Angle : 0.962 13.924 6011 Z= 0.471 Chirality : 0.050 0.225 711 Planarity : 0.006 0.051 585 Dihedral : 23.242 162.674 1158 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 33.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.99 % Favored : 88.74 % Rotamer: Outliers : 5.31 % Allowed : 35.10 % 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: -2.80 (0.42), residues: 373 helix: -0.81 (0.44), residues: 116 sheet: -1.54 (0.65), residues: 80 loop : -2.75 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 745 HIS 0.004 0.001 HIS A 943 PHE 0.017 0.002 PHE A 985 TYR 0.041 0.003 TYR A 669 ARG 0.005 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 81 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.352 Fit side-chains REVERT: A 844 GLU cc_start: 0.3057 (OUTLIER) cc_final: 0.2695 (mp0) REVERT: A 948 TRP cc_start: 0.8512 (t-100) cc_final: 0.7865 (t-100) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.1608 time to fit residues: 15.6421 Evaluate side-chains 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 684 VAL Chi-restraints excluded: chain A residue 718 THR 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 790 THR Chi-restraints excluded: chain A residue 818 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.174856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.152933 restraints weight = 12575.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.157834 restraints weight = 7946.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.161248 restraints weight = 5537.895| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4271 Z= 0.212 Angle : 0.849 14.424 6011 Z= 0.406 Chirality : 0.045 0.191 711 Planarity : 0.005 0.051 585 Dihedral : 22.496 153.825 1158 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.04 % Favored : 91.69 % Rotamer: Outliers : 4.42 % Allowed : 37.17 % 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: -2.25 (0.44), residues: 373 helix: -0.27 (0.47), residues: 117 sheet: -0.85 (0.68), residues: 76 loop : -2.70 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 PHE 0.016 0.002 PHE A 852 TYR 0.036 0.002 TYR A 669 ARG 0.005 0.001 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 77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 673 LEU cc_start: 0.6861 (mm) cc_final: 0.6451 (mm) REVERT: A 683 MET cc_start: -0.0862 (ttt) cc_final: -0.1210 (ptm) outliers start: 15 outliers final: 14 residues processed: 74 average time/residue: 0.1564 time to fit residues: 14.6593 Evaluate side-chains 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 682 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 50.0000 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.171734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.149635 restraints weight = 12618.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.154528 restraints weight = 7919.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.158045 restraints weight = 5496.148| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4271 Z= 0.262 Angle : 0.889 14.366 6011 Z= 0.427 Chirality : 0.046 0.197 711 Planarity : 0.005 0.052 585 Dihedral : 22.685 155.741 1158 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.65 % Favored : 90.08 % Rotamer: Outliers : 4.13 % Allowed : 37.46 % 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: -2.35 (0.43), residues: 373 helix: -0.21 (0.47), residues: 110 sheet: -1.00 (0.66), residues: 78 loop : -2.74 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 PHE 0.012 0.002 PHE A 638 TYR 0.034 0.003 TYR A 669 ARG 0.006 0.001 ARG A 829 ********************** 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 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 669 TYR cc_start: 0.7307 (t80) cc_final: 0.6684 (t80) outliers start: 14 outliers final: 14 residues processed: 71 average time/residue: 0.1663 time to fit residues: 14.9509 Evaluate side-chains 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 682 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.0170 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** 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 = 0.4500 r_free = 0.4500 target = 0.177560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.155887 restraints weight = 12356.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.160770 restraints weight = 7748.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.164249 restraints weight = 5399.521| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4271 Z= 0.198 Angle : 0.836 14.257 6011 Z= 0.397 Chirality : 0.045 0.195 711 Planarity : 0.005 0.051 585 Dihedral : 22.389 152.937 1158 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.77 % Favored : 91.96 % Rotamer: Outliers : 5.60 % Allowed : 35.10 % 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: -2.25 (0.44), residues: 373 helix: -0.24 (0.48), residues: 113 sheet: -0.79 (0.66), residues: 77 loop : -2.70 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 745 HIS 0.002 0.001 HIS A 943 PHE 0.016 0.002 PHE A 852 TYR 0.030 0.002 TYR A 669 ARG 0.007 0.001 ARG A 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.06 seconds wall clock time: 29 minutes 24.70 seconds (1764.70 seconds total)