Starting phenix.real_space_refine on Wed Mar 5 22:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiz_60610/03_2025/9iiz_60610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiz_60610/03_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_60610/03_2025/9iiz_60610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiz_60610/03_2025/9iiz_60610.map" model { file = "/net/cci-nas-00/data/ceres_data/9iiz_60610/03_2025/9iiz_60610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiz_60610/03_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-5624/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: 3.20, per 1000 atoms: 0.78 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: 1.06 Conformation dependent library (CDL) restraints added in 373.6 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: 1.56 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: 1.41 Time building geometry restraints manager: 1.26 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.510 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- 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 : 0.375 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: 0.2014 time to fit residues: 16.5591 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 : 0.373 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.155994 restraints weight = 11731.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.160930 restraints weight = 7312.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.164373 restraints weight = 5054.733| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 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 : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5046 (tmm) cc_final: 0.4777 (tmm) REVERT: A 674 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6533 (ttm170) REVERT: A 748 GLU cc_start: 0.8316 (pp20) cc_final: 0.8082 (pp20) outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.2126 time to fit residues: 17.9365 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 : 0.392 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 40 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.175124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.153644 restraints weight = 11904.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.158420 restraints weight = 7629.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.161731 restraints weight = 5336.798| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4271 Z= 0.245 Angle : 0.817 12.564 6011 Z= 0.392 Chirality : 0.044 0.207 711 Planarity : 0.005 0.049 585 Dihedral : 22.817 159.853 1159 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.72 % Allowed : 28.61 % 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: -2.50 (0.42), residues: 373 helix: -0.57 (0.45), residues: 116 sheet: -1.32 (0.60), residues: 78 loop : -2.59 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 745 HIS 0.018 0.002 HIS A 962 PHE 0.011 0.002 PHE A 985 TYR 0.011 0.002 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 81 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.5081 (tpt) cc_final: 0.4626 (tpt) REVERT: A 674 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6387 (ttm170) REVERT: A 723 GLN cc_start: 0.8200 (pp30) cc_final: 0.7934 (pp30) REVERT: A 726 ARG cc_start: 0.8309 (mmt180) cc_final: 0.7950 (tpp-160) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.1977 time to fit residues: 18.0877 Evaluate side-chains 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 909 HIS 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: 2.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.179466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.158630 restraints weight = 11920.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.163286 restraints weight = 7508.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.166634 restraints weight = 5198.989| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.2560 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= 0.180 Angle : 0.749 11.237 6011 Z= 0.357 Chirality : 0.043 0.192 711 Planarity : 0.005 0.047 585 Dihedral : 22.448 154.493 1159 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.24 % Allowed : 32.74 % Favored : 64.01 % 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: -2.28 (0.43), residues: 373 helix: -0.29 (0.47), residues: 116 sheet: -1.28 (0.60), residues: 80 loop : -2.48 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.009 0.001 HIS A 962 PHE 0.010 0.001 PHE A 985 TYR 0.008 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 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4649 (tpt) cc_final: 0.4279 (tpt) REVERT: A 723 GLN cc_start: 0.8098 (pp30) cc_final: 0.7883 (pp30) REVERT: A 726 ARG cc_start: 0.8275 (mmt180) cc_final: 0.7941 (tpp-160) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.1914 time to fit residues: 16.5638 Evaluate side-chains 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 SER 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 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: 3.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.0060 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.2200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.172528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.150118 restraints weight = 12533.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.155135 restraints weight = 7838.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.158592 restraints weight = 5449.346| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4271 Z= 0.264 Angle : 0.801 10.939 6011 Z= 0.391 Chirality : 0.046 0.262 711 Planarity : 0.005 0.051 585 Dihedral : 22.641 158.034 1158 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 6.19 % Allowed : 32.15 % Favored : 61.65 % 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: -0.21 (0.48), residues: 115 sheet: -1.29 (0.60), residues: 80 loop : -2.56 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 745 HIS 0.008 0.001 HIS A 962 PHE 0.012 0.002 PHE A 985 TYR 0.013 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 85 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.5473 (tpt) cc_final: 0.5147 (tpt) REVERT: A 673 LEU cc_start: 0.7261 (mt) cc_final: 0.7037 (mt) REVERT: A 723 GLN cc_start: 0.8133 (pp30) cc_final: 0.7805 (pp30) REVERT: A 844 GLU cc_start: 0.2762 (OUTLIER) cc_final: 0.2190 (mp0) outliers start: 21 outliers final: 17 residues processed: 78 average time/residue: 0.1814 time to fit residues: 17.3820 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 : 0.356 ------------------------------------------------------------------------------- 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 674 ARG 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 962 HIS Chi-restraints excluded: chain A residue 967 LEU 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: 0.4980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 26 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.178948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.157077 restraints weight = 11964.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.161817 restraints weight = 7564.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.165147 restraints weight = 5299.615| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3086 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= 0.183 Angle : 0.744 11.381 6011 Z= 0.357 Chirality : 0.043 0.206 711 Planarity : 0.005 0.049 585 Dihedral : 22.255 153.325 1158 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.42 % Allowed : 33.33 % Favored : 62.24 % 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: -0.08 (0.49), residues: 116 sheet: -1.13 (0.62), residues: 80 loop : -2.49 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 745 HIS 0.011 0.001 HIS A 962 PHE 0.013 0.001 PHE A 985 TYR 0.029 0.002 TYR A 669 ARG 0.008 0.000 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 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLN cc_start: 0.8018 (pp30) cc_final: 0.7769 (pp30) REVERT: A 726 ARG cc_start: 0.8200 (mmt180) cc_final: 0.7802 (tpp-160) REVERT: A 844 GLU cc_start: 0.2776 (OUTLIER) cc_final: 0.2191 (mp0) outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 0.1820 time to fit residues: 15.9704 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 : 0.335 ------------------------------------------------------------------------------- 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 790 THR 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 915 VAL Chi-restraints excluded: chain A residue 943 HIS Chi-restraints excluded: chain A residue 962 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 38 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 31 optimal weight: 0.2980 chunk 9 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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** A 962 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.179697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.158948 restraints weight = 12383.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.163827 restraints weight = 7682.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.167341 restraints weight = 5261.831| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4271 Z= 0.173 Angle : 0.736 13.068 6011 Z= 0.354 Chirality : 0.043 0.205 711 Planarity : 0.005 0.048 585 Dihedral : 22.135 151.899 1158 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.72 % Allowed : 35.40 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.44), residues: 373 helix: 0.29 (0.51), residues: 110 sheet: -0.91 (0.62), residues: 78 loop : -2.59 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 745 HIS 0.003 0.001 HIS A 909 PHE 0.009 0.001 PHE A 985 TYR 0.025 0.002 TYR A 669 ARG 0.008 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 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8873 (tppp) cc_final: 0.8637 (tppt) REVERT: A 651 MET cc_start: 0.4951 (tpt) cc_final: 0.4501 (tpt) REVERT: A 726 ARG cc_start: 0.8204 (mmt180) cc_final: 0.7615 (tpp80) REVERT: A 844 GLU cc_start: 0.2733 (OUTLIER) cc_final: 0.2221 (mp0) outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 0.1640 time to fit residues: 14.7641 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 : 0.382 ------------------------------------------------------------------------------- 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 687 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 818 ASN Chi-restraints excluded: chain A residue 844 GLU 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 962 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 0 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** A 962 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.171405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.150495 restraints weight = 12566.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.155008 restraints weight = 7968.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.158231 restraints weight = 5577.860| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4271 Z= 0.293 Angle : 0.854 12.467 6011 Z= 0.418 Chirality : 0.046 0.207 711 Planarity : 0.006 0.082 585 Dihedral : 22.624 156.466 1158 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 6.19 % Allowed : 35.10 % Favored : 58.70 % 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: -2.27 (0.42), residues: 373 helix: -0.09 (0.48), residues: 111 sheet: -0.99 (0.64), residues: 77 loop : -2.71 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 745 HIS 0.012 0.001 HIS A 962 PHE 0.012 0.002 PHE A 985 TYR 0.025 0.002 TYR A 669 ARG 0.012 0.001 ARG A 921 *********************** 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 84 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 MET cc_start: 0.0704 (ptm) cc_final: -0.0121 (ptm) REVERT: A 844 GLU cc_start: 0.2784 (OUTLIER) cc_final: 0.2179 (mp0) outliers start: 21 outliers final: 16 residues processed: 78 average time/residue: 0.2632 time to fit residues: 25.8245 Evaluate side-chains 79 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 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 962 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 9 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** A 962 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.174026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153163 restraints weight = 12708.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.157841 restraints weight = 8018.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.161082 restraints weight = 5565.610| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4271 Z= 0.226 Angle : 0.838 15.899 6011 Z= 0.397 Chirality : 0.045 0.201 711 Planarity : 0.005 0.050 585 Dihedral : 22.456 154.619 1158 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.58 % Favored : 91.15 % Rotamer: Outliers : 5.60 % Allowed : 35.40 % Favored : 59.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.43), residues: 373 helix: -0.01 (0.49), residues: 111 sheet: -1.01 (0.65), residues: 77 loop : -2.66 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 745 HIS 0.004 0.001 HIS A 962 PHE 0.010 0.002 PHE A 852 TYR 0.036 0.002 TYR A 669 ARG 0.007 0.001 ARG A 921 *********************** 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 81 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 GLU cc_start: 0.2917 (OUTLIER) cc_final: 0.2353 (mp0) outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.1444 time to fit residues: 14.2642 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 : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 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 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 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 914 THR 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 967 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 0.0970 chunk 0 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** A 962 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.177185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.156554 restraints weight = 12557.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.161212 restraints weight = 7955.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.164561 restraints weight = 5538.697| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.3770 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= 0.195 Angle : 0.829 15.758 6011 Z= 0.390 Chirality : 0.045 0.195 711 Planarity : 0.005 0.049 585 Dihedral : 22.253 152.507 1158 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.12 % Favored : 90.62 % Rotamer: Outliers : 5.01 % Allowed : 35.99 % Favored : 59.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.44), residues: 373 helix: 0.17 (0.50), residues: 110 sheet: -0.98 (0.64), residues: 77 loop : -2.68 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 745 HIS 0.007 0.001 HIS A 962 PHE 0.011 0.001 PHE A 852 TYR 0.032 0.002 TYR A 669 ARG 0.006 0.001 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 80 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 673 LEU cc_start: 0.7034 (mm) cc_final: 0.6733 (mm) REVERT: A 683 MET cc_start: 0.0405 (tmm) cc_final: -0.0112 (ptm) REVERT: A 726 ARG cc_start: 0.8169 (mmt180) cc_final: 0.7962 (tpp-160) REVERT: A 844 GLU cc_start: 0.2841 (OUTLIER) cc_final: 0.2286 (mp0) REVERT: A 906 VAL cc_start: 0.2958 (OUTLIER) cc_final: 0.1339 (t) REVERT: A 921 ARG cc_start: 0.8136 (tpm170) cc_final: 0.7708 (ptm160) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1477 time to fit residues: 14.2650 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 676 LEU 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 790 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 962 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 10 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.177681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.157569 restraints weight = 12428.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.162389 restraints weight = 7748.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.165659 restraints weight = 5257.072| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.3881 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= 0.194 Angle : 0.824 15.693 6011 Z= 0.386 Chirality : 0.045 0.197 711 Planarity : 0.005 0.049 585 Dihedral : 22.186 151.655 1158 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.04 % Favored : 91.69 % Rotamer: Outliers : 4.72 % Allowed : 35.69 % 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: -2.09 (0.44), residues: 373 helix: 0.30 (0.51), residues: 110 sheet: -1.01 (0.64), residues: 77 loop : -2.70 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 745 HIS 0.005 0.001 HIS A 962 PHE 0.010 0.001 PHE A 852 TYR 0.036 0.002 TYR A 669 ARG 0.006 0.000 ARG A 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.36 seconds wall clock time: 29 minutes 32.85 seconds (1772.85 seconds total)