Starting phenix.real_space_refine on Tue Aug 4 14:31:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiz_60610/08_2026/9iiz_60610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiz_60610/08_2026/9iiz_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 { model { file = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2026/9iiz_60610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2026/9iiz_60610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2026/9iiz_60610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiz_60610/08_2026/9iiz_60610.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 1.18, per 1000 atoms: 0.29 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: 0.35 Conformation dependent library (CDL) restraints added in 110.2 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: 0.43 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: 0.45 Time building geometry restraints manager: 0.47 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 1.00e-02 1.00e+04 1.02e+01 bond pdb=" N1 C C 12 " pdb=" C2 C C 12 " ideal model delta sigma weight residual 1.397 1.423 -0.026 1.00e-02 1.00e+04 6.61e+00 bond pdb=" P U B 25 " pdb=" O5' U B 25 " ideal model delta sigma weight residual 1.593 1.616 -0.023 1.00e-02 1.00e+04 5.28e+00 bond pdb=" N1 C B 5 " pdb=" C2 C B 5 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 4.65e+00 bond pdb=" C3' U B 1 " pdb=" O3' U B 1 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.20e-02 6.94e+03 3.95e+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=" C1' C C 12 " pdb=" N1 C C 12 " pdb=" C2 C C 12 " ideal model delta sigma weight residual 118.80 127.19 -8.39 1.10e+00 8.26e-01 5.81e+01 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=" C3' U B 1 " pdb=" O3' U B 1 " pdb=" P U B 2 " ideal model delta sigma weight residual 119.70 127.73 -8.03 1.20e+00 6.94e-01 4.48e+01 angle pdb=" C1' C B 5 " pdb=" N1 C B 5 " pdb=" C2 C B 5 " ideal model delta sigma weight residual 118.80 126.10 -7.30 1.10e+00 8.26e-01 4.40e+01 angle pdb=" N1 C C 12 " pdb=" C2 C C 12 " pdb=" O2 C C 12 " ideal model delta sigma weight residual 118.90 122.68 -3.78 6.00e-01 2.78e+00 3.98e+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: 619 0.112 - 0.223: 86 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.870 Find NCS groups from input model: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 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= 0.333 Angle : 1.279 18.610 6011 Z= 0.862 Chirality : 0.075 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 726 TYR 0.024 0.002 TYR A 901 PHE 0.037 0.002 PHE A 986 TRP 0.022 0.003 TRP A 745 HIS 0.004 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.33 ( 4271) covalent geometry : angle 1.27934 / 0.86 ( 6011) hydrogen bonds : bond 0.15622 / 9.81 ( 152) hydrogen bonds : angle 7.60011 / 4.99 ( 396) *********************** 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 : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 MET cc_start: -0.2982 (ptt) cc_final: -0.3285 (ptt) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.0622 time to fit residues: 5.1714 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 : 0.071 ------------------------------------------------------------------------------- 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 24 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.0000 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 600 ASN ** 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 = 0.4535 r_free = 0.4535 target = 0.183503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.162059 restraints weight = 12118.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.166727 restraints weight = 7654.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.169973 restraints weight = 5285.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.172457 restraints weight = 3909.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.174319 restraints weight = 3014.235| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4271 Z= 0.142 Angle : 0.739 11.514 6011 Z= 0.389 Chirality : 0.048 0.406 711 Planarity : 0.006 0.047 585 Dihedral : 22.657 162.646 1160 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.06 % Allowed : 28.61 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.40), residues: 373 helix: -1.36 (0.43), residues: 118 sheet: -0.76 (0.61), residues: 74 loop : -2.88 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 726 TYR 0.009 0.001 TYR A 787 PHE 0.012 0.001 PHE A 638 TRP 0.009 0.001 TRP A 605 HIS 0.002 0.000 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 4271) covalent geometry : angle 0.73919 / 0.39 ( 6011) hydrogen bonds : bond 0.08384 / 5.76 ( 152) hydrogen bonds : angle 5.69430 / 3.89 ( 396) *********************** 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 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 736 MET cc_start: 0.8090 (mpp) cc_final: 0.7735 (mpp) REVERT: A 748 GLU cc_start: 0.8074 (pp20) cc_final: 0.7869 (pp20) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.0579 time to fit residues: 4.6780 Evaluate side-chains 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 959 ASN 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 18 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 37 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4481 r_free = 0.4481 target = 0.179145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.157699 restraints weight = 11873.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.162475 restraints weight = 7457.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.165846 restraints weight = 5168.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.168360 restraints weight = 3815.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.170114 restraints weight = 2917.575| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4271 Z= 0.171 Angle : 0.733 11.498 6011 Z= 0.383 Chirality : 0.047 0.391 711 Planarity : 0.005 0.046 585 Dihedral : 22.714 160.929 1159 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.95 % Allowed : 29.79 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.41), residues: 373 helix: -0.93 (0.44), residues: 119 sheet: -1.26 (0.61), residues: 78 loop : -2.68 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 726 TYR 0.017 0.001 TYR A 669 PHE 0.011 0.001 PHE A 638 TRP 0.008 0.001 TRP A 786 HIS 0.005 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 4271) covalent geometry : angle 0.73261 / 0.38 ( 6011) hydrogen bonds : bond 0.08567 / 5.82 ( 152) hydrogen bonds : angle 5.56303 / 3.84 ( 396) *********************** 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 77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 674 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6422 (ttm170) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.0867 time to fit residues: 7.5786 Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 761 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 962 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4436 r_free = 0.4436 target = 0.174652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.153487 restraints weight = 12152.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.158174 restraints weight = 7670.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.161438 restraints weight = 5312.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.163698 restraints weight = 3933.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.165472 restraints weight = 3074.983| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4271 Z= 0.238 Angle : 0.812 12.265 6011 Z= 0.428 Chirality : 0.050 0.404 711 Planarity : 0.006 0.049 585 Dihedral : 22.906 163.275 1159 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.72 % Allowed : 30.38 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.42), residues: 373 helix: -0.67 (0.45), residues: 116 sheet: -1.42 (0.62), residues: 76 loop : -2.58 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 671 TYR 0.027 0.002 TYR A 669 PHE 0.013 0.002 PHE A 638 TRP 0.010 0.002 TRP A 623 HIS 0.010 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.24 ( 4271) covalent geometry : angle 0.81220 / 0.43 ( 6011) hydrogen bonds : bond 0.09598 / 6.60 ( 152) hydrogen bonds : angle 5.77899 / 4.02 ( 396) *********************** 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 80 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4811 (tpt) cc_final: 0.4403 (tpt) REVERT: A 674 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6454 (ttm170) REVERT: A 683 MET cc_start: 0.1262 (ttt) cc_final: 0.0870 (ttt) REVERT: A 699 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7841 (m) REVERT: A 726 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7930 (tpp-160) REVERT: A 736 MET cc_start: 0.8209 (mpp) cc_final: 0.7941 (mpp) outliers start: 16 outliers final: 11 residues processed: 75 average time/residue: 0.0879 time to fit residues: 8.0325 Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 687 VAL Chi-restraints excluded: chain A residue 699 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4481 r_free = 0.4481 target = 0.179102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.157628 restraints weight = 12036.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.162462 restraints weight = 7575.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.165749 restraints weight = 5243.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.168161 restraints weight = 3868.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.169942 restraints weight = 2985.149| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4271 Z= 0.152 Angle : 0.742 12.354 6011 Z= 0.382 Chirality : 0.047 0.395 711 Planarity : 0.005 0.048 585 Dihedral : 22.777 162.720 1159 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.54 % Allowed : 32.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.43), residues: 373 helix: -0.42 (0.47), residues: 116 sheet: -1.24 (0.61), residues: 78 loop : -2.54 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 671 TYR 0.028 0.002 TYR A 669 PHE 0.009 0.001 PHE A 985 TRP 0.009 0.001 TRP A 745 HIS 0.003 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 4271) covalent geometry : angle 0.74211 / 0.38 ( 6011) hydrogen bonds : bond 0.06947 / 4.81 ( 152) hydrogen bonds : angle 5.49020 / 3.81 ( 396) *********************** 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 76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4574 (tpt) cc_final: 0.4337 (tpt) REVERT: A 683 MET cc_start: 0.0922 (ttt) cc_final: 0.0488 (ttt) REVERT: A 726 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7893 (mmm160) outliers start: 12 outliers final: 7 residues processed: 71 average time/residue: 0.0684 time to fit residues: 6.0453 Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 761 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 987 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4487 r_free = 0.4487 target = 0.179468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.158182 restraints weight = 11988.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.162921 restraints weight = 7656.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.166258 restraints weight = 5331.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.168777 restraints weight = 3926.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.170645 restraints weight = 3010.260| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4271 Z= 0.154 Angle : 0.783 13.494 6011 Z= 0.399 Chirality : 0.048 0.388 711 Planarity : 0.005 0.049 585 Dihedral : 22.606 161.186 1158 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.13 % Allowed : 31.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.43), residues: 373 helix: -0.17 (0.47), residues: 116 sheet: -1.21 (0.61), residues: 78 loop : -2.53 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.010 0.001 TYR A 669 PHE 0.009 0.001 PHE A 985 TRP 0.012 0.001 TRP A 745 HIS 0.018 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 4271) covalent geometry : angle 0.78344 / 0.40 ( 6011) hydrogen bonds : bond 0.07183 / 5.05 ( 152) hydrogen bonds : angle 5.54168 / 3.85 ( 396) *********************** 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 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4616 (tpt) cc_final: 0.4374 (tpt) REVERT: A 683 MET cc_start: 0.1619 (ttt) cc_final: 0.1261 (ttt) outliers start: 14 outliers final: 12 residues processed: 70 average time/residue: 0.0793 time to fit residues: 6.8859 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 : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS 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 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 THR 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 987 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 0.0270 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4482 r_free = 0.4482 target = 0.178915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.157418 restraints weight = 12246.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.162245 restraints weight = 7820.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.165677 restraints weight = 5432.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.168232 restraints weight = 4000.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.170168 restraints weight = 3070.224| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.2441 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= 0.149 Angle : 0.761 12.954 6011 Z= 0.390 Chirality : 0.048 0.391 711 Planarity : 0.005 0.049 585 Dihedral : 22.549 160.870 1158 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.04 % Favored : 91.69 % Rotamer: Outliers : 4.72 % Allowed : 32.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.43), residues: 373 helix: -0.24 (0.48), residues: 116 sheet: -1.18 (0.62), residues: 78 loop : -2.58 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 671 TYR 0.009 0.001 TYR A 669 PHE 0.009 0.001 PHE A 985 TRP 0.013 0.002 TRP A 745 HIS 0.004 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 4271) covalent geometry : angle 0.76141 / 0.39 ( 6011) hydrogen bonds : bond 0.07065 / 4.82 ( 152) hydrogen bonds : angle 5.49553 / 3.82 ( 396) *********************** 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 80 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: A 651 MET cc_start: 0.4804 (tpt) cc_final: 0.4542 (tpt) REVERT: A 726 ARG cc_start: 0.8150 (mmt180) cc_final: 0.7873 (tpp-160) REVERT: A 844 GLU cc_start: 0.2515 (OUTLIER) cc_final: 0.1963 (mp0) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.0757 time to fit residues: 7.0981 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 : 0.121 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 962 HIS Chi-restraints excluded: chain A residue 987 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 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 = 0.4456 r_free = 0.4456 target = 0.176628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.155119 restraints weight = 12132.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.159676 restraints weight = 7728.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.162988 restraints weight = 5454.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.165442 restraints weight = 4081.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.167307 restraints weight = 3176.916| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4271 Z= 0.192 Angle : 0.830 14.647 6011 Z= 0.420 Chirality : 0.050 0.403 711 Planarity : 0.005 0.049 585 Dihedral : 22.604 161.801 1158 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.85 % Favored : 90.88 % Rotamer: Outliers : 5.01 % Allowed : 32.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.43), residues: 373 helix: -0.21 (0.48), residues: 116 sheet: -1.28 (0.60), residues: 80 loop : -2.51 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 671 TYR 0.058 0.002 TYR A 669 PHE 0.010 0.002 PHE A 985 TRP 0.012 0.002 TRP A 745 HIS 0.023 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 4271) covalent geometry : angle 0.82992 / 0.42 ( 6011) hydrogen bonds : bond 0.07794 / 5.39 ( 152) hydrogen bonds : angle 5.62620 / 3.91 ( 396) *********************** 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 77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.4679 (tmm) cc_final: 0.4364 (tmm) REVERT: A 651 MET cc_start: 0.4974 (tpt) cc_final: 0.4715 (tpt) REVERT: A 844 GLU cc_start: 0.2605 (OUTLIER) cc_final: 0.2046 (mp0) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.0732 time to fit residues: 6.7012 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 : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4469 r_free = 0.4469 target = 0.176883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.155202 restraints weight = 12281.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.159851 restraints weight = 7790.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.163061 restraints weight = 5471.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.165628 restraints weight = 4123.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.167497 restraints weight = 3185.660| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4271 Z= 0.174 Angle : 0.819 13.931 6011 Z= 0.412 Chirality : 0.049 0.404 711 Planarity : 0.005 0.049 585 Dihedral : 22.607 162.074 1158 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 5.60 % Allowed : 32.45 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.43), residues: 373 helix: -0.40 (0.48), residues: 116 sheet: -1.30 (0.61), residues: 80 loop : -2.49 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.051 0.002 TYR A 669 PHE 0.011 0.002 PHE A 986 TRP 0.031 0.003 TRP A 745 HIS 0.004 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 4271) covalent geometry : angle 0.81891 / 0.41 ( 6011) hydrogen bonds : bond 0.07234 / 4.98 ( 152) hydrogen bonds : angle 5.57442 / 3.89 ( 396) *********************** 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 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.4636 (tmm) cc_final: 0.4276 (tmm) REVERT: A 608 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: A 651 MET cc_start: 0.5092 (tpt) cc_final: 0.4831 (tpt) REVERT: A 844 GLU cc_start: 0.2605 (OUTLIER) cc_final: 0.2035 (mp0) outliers start: 19 outliers final: 14 residues processed: 73 average time/residue: 0.0686 time to fit residues: 6.3332 Evaluate side-chains 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 20.0000 chunk 9 optimal weight: 0.2980 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4501 r_free = 0.4501 target = 0.179540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.158030 restraints weight = 11956.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.162754 restraints weight = 7650.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.166214 restraints weight = 5341.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.168549 restraints weight = 3933.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.170449 restraints weight = 3051.456| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4271 Z= 0.157 Angle : 0.812 15.481 6011 Z= 0.402 Chirality : 0.048 0.389 711 Planarity : 0.005 0.049 585 Dihedral : 22.434 160.553 1158 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.13 % Allowed : 34.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.44), residues: 373 helix: -0.27 (0.49), residues: 116 sheet: -1.36 (0.60), residues: 80 loop : -2.54 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.055 0.002 TYR A 960 PHE 0.018 0.002 PHE A 986 TRP 0.028 0.002 TRP A 745 HIS 0.015 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 4271) covalent geometry : angle 0.81228 / 0.40 ( 6011) hydrogen bonds : bond 0.06552 / 4.63 ( 152) hydrogen bonds : angle 5.50104 / 3.83 ( 396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.4561 (tmm) cc_final: 0.4329 (tmm) REVERT: A 608 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: A 651 MET cc_start: 0.4954 (tpt) cc_final: 0.4694 (tpt) REVERT: A 726 ARG cc_start: 0.8258 (mmt180) cc_final: 0.7949 (tpp-160) REVERT: A 921 ARG cc_start: 0.8146 (tpm170) cc_final: 0.7804 (ptp-170) outliers start: 14 outliers final: 12 residues processed: 70 average time/residue: 0.0799 time to fit residues: 6.8900 Evaluate side-chains 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 GLU 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 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 959 ASN Chi-restraints excluded: chain A residue 962 HIS Chi-restraints excluded: chain A residue 987 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.0870 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 0.0070 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4534 r_free = 0.4534 target = 0.181623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.160505 restraints weight = 11825.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.165201 restraints weight = 7594.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.168573 restraints weight = 5332.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.170998 restraints weight = 3933.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.172782 restraints weight = 3027.637| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.2919 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= 0.143 Angle : 0.813 14.785 6011 Z= 0.401 Chirality : 0.048 0.378 711 Planarity : 0.005 0.050 585 Dihedral : 22.266 158.918 1158 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.54 % Allowed : 34.51 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.43), residues: 373 helix: -0.35 (0.48), residues: 116 sheet: -1.33 (0.60), residues: 80 loop : -2.61 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 671 TYR 0.039 0.002 TYR A 960 PHE 0.010 0.001 PHE A 985 TRP 0.028 0.002 TRP A 745 HIS 0.009 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 4271) covalent geometry : angle 0.81263 / 0.40 ( 6011) hydrogen bonds : bond 0.06195 / 4.32 ( 152) hydrogen bonds : angle 5.42486 / 3.76 ( 396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 911.81 seconds wall clock time: 16 minutes 30.19 seconds (990.19 seconds total)