Starting phenix.real_space_refine on Wed Jul 1 23:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiz_60610/07_2026/9iiz_60610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiz_60610/07_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_60610/07_2026/9iiz_60610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiz_60610/07_2026/9iiz_60610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iiz_60610/07_2026/9iiz_60610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiz_60610/07_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-dev-6108/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: 1.13, per 1000 atoms: 0.28 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: 0.36 Conformation dependent library (CDL) restraints added in 112.5 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: 0.42 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: 0.77 Time building geometry restraints manager: 0.48 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=" 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=" 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=" 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 ... (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=" 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 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 ... (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: 658 0.112 - 0.223: 47 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.950 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.550 ------------------------------------------------------------------------------- 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= 0.320 Angle : 1.236 18.610 6011 Z= 0.821 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 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 0.00521 / 0.32 ( 4271) covalent geometry : angle 1.23569 / 0.82 ( 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 : 0.091 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: 0.0630 time to fit residues: 5.2741 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 : 0.075 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.183269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.161843 restraints weight = 12072.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.166483 restraints weight = 7594.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.169836 restraints weight = 5245.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.172250 restraints weight = 3845.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.174138 restraints weight = 2969.078| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4271 Z= 0.142 Angle : 0.720 10.756 6011 Z= 0.386 Chirality : 0.045 0.227 711 Planarity : 0.005 0.046 585 Dihedral : 22.778 160.997 1160 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.06 % Allowed : 28.02 % Favored : 69.91 % 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: -2.89 (0.40), residues: 373 helix: -1.35 (0.43), residues: 118 sheet: -0.78 (0.61), residues: 74 loop : -2.85 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 726 TYR 0.009 0.001 TYR A 787 PHE 0.011 0.001 PHE A 638 TRP 0.008 0.001 TRP A 745 HIS 0.003 0.000 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 4271) covalent geometry : angle 0.72032 / 0.39 ( 6011) hydrogen bonds : bond 0.08020 / 5.53 ( 152) hydrogen bonds : angle 5.61030 / 3.84 ( 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 : 0.131 Fit side-chains revert: symmetry clash REVERT: A 736 MET cc_start: 0.8070 (mpp) cc_final: 0.7684 (mpp) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.0678 time to fit residues: 5.5240 Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.0030 chunk 37 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.178388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.157340 restraints weight = 11946.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.161986 restraints weight = 7414.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.165292 restraints weight = 5123.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.167802 restraints weight = 3789.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.169528 restraints weight = 2892.949| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4271 Z= 0.180 Angle : 0.734 11.282 6011 Z= 0.389 Chirality : 0.045 0.227 711 Planarity : 0.005 0.046 585 Dihedral : 22.849 158.504 1159 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.24 % Allowed : 30.38 % Favored : 66.37 % 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: -2.62 (0.41), residues: 373 helix: -0.78 (0.45), residues: 116 sheet: -1.27 (0.61), residues: 78 loop : -2.64 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 671 TYR 0.016 0.001 TYR A 669 PHE 0.011 0.001 PHE A 638 TRP 0.009 0.002 TRP A 786 HIS 0.012 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 4271) covalent geometry : angle 0.73412 / 0.39 ( 6011) hydrogen bonds : bond 0.08433 / 5.71 ( 152) hydrogen bonds : angle 5.54763 / 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 79 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 674 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6404 (ttm170) outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 0.0828 time to fit residues: 7.2878 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 : 0.091 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.177244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.155694 restraints weight = 11981.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.160510 restraints weight = 7544.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.163823 restraints weight = 5218.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.166247 restraints weight = 3860.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.168033 restraints weight = 2985.929| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4271 Z= 0.185 Angle : 0.750 11.840 6011 Z= 0.398 Chirality : 0.046 0.223 711 Planarity : 0.005 0.045 585 Dihedral : 22.870 159.405 1159 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % 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: -2.50 (0.42), residues: 373 helix: -0.69 (0.45), residues: 116 sheet: -1.31 (0.61), residues: 78 loop : -2.49 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 671 TYR 0.025 0.001 TYR A 669 PHE 0.010 0.001 PHE A 638 TRP 0.008 0.002 TRP A 786 HIS 0.011 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 ( 4271) covalent geometry : angle 0.74999 / 0.40 ( 6011) hydrogen bonds : bond 0.07892 / 5.36 ( 152) hydrogen bonds : angle 5.54331 / 3.84 ( 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 79 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4475 (tpt) cc_final: 0.4069 (tpt) REVERT: A 674 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6452 (ttm170) REVERT: A 683 MET cc_start: 0.0996 (ttt) cc_final: 0.0542 (ttt) REVERT: A 699 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7744 (m) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.0790 time to fit residues: 7.1341 Evaluate side-chains 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 915 VAL 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: 3.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.179933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.158405 restraints weight = 11819.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.163087 restraints weight = 7592.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.166356 restraints weight = 5336.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.168740 restraints weight = 3982.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.170606 restraints weight = 3103.055| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4271 Z= 0.139 Angle : 0.727 12.592 6011 Z= 0.378 Chirality : 0.045 0.196 711 Planarity : 0.005 0.048 585 Dihedral : 22.747 158.459 1159 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.54 % Allowed : 33.63 % Favored : 62.83 % 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: -2.37 (0.43), residues: 373 helix: -0.50 (0.46), residues: 116 sheet: -1.22 (0.61), residues: 78 loop : -2.49 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 671 TYR 0.032 0.002 TYR A 669 PHE 0.009 0.001 PHE A 985 TRP 0.010 0.001 TRP A 745 HIS 0.002 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 4271) covalent geometry : angle 0.72708 / 0.38 ( 6011) hydrogen bonds : bond 0.06606 / 4.55 ( 152) hydrogen bonds : angle 5.41370 / 3.73 ( 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 79 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4485 (tpt) cc_final: 0.4134 (tpt) REVERT: A 726 ARG cc_start: 0.8147 (mmt180) cc_final: 0.7815 (mmm160) outliers start: 12 outliers final: 7 residues processed: 74 average time/residue: 0.0650 time to fit residues: 5.9594 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 : 0.119 ------------------------------------------------------------------------------- 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 776 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL 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: 0.9990 chunk 14 optimal weight: 0.0470 chunk 31 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.180998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.159704 restraints weight = 12111.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.164347 restraints weight = 7811.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.167687 restraints weight = 5467.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.170022 restraints weight = 4067.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.171853 restraints weight = 3181.388| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.2214 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= 0.138 Angle : 0.732 11.901 6011 Z= 0.380 Chirality : 0.045 0.202 711 Planarity : 0.005 0.048 585 Dihedral : 22.582 157.065 1158 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.24 % Allowed : 34.22 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.21 (0.43), residues: 373 helix: -0.23 (0.47), residues: 116 sheet: -1.23 (0.60), residues: 80 loop : -2.45 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 671 TYR 0.043 0.002 TYR A 669 PHE 0.009 0.001 PHE A 985 TRP 0.011 0.001 TRP A 745 HIS 0.004 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 4271) covalent geometry : angle 0.73227 / 0.38 ( 6011) hydrogen bonds : bond 0.06442 / 4.43 ( 152) hydrogen bonds : angle 5.33842 / 3.71 ( 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 76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.4458 (tpt) cc_final: 0.4139 (tpt) REVERT: A 726 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7881 (tpp-160) REVERT: A 921 ARG cc_start: 0.8152 (tpm170) cc_final: 0.7867 (ptp-110) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.0688 time to fit residues: 5.9486 Evaluate side-chains 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 HIS 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 915 VAL 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: 1.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.176147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.154485 restraints weight = 12465.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.159305 restraints weight = 7888.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.162740 restraints weight = 5490.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.165244 restraints weight = 4059.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.167109 restraints weight = 3136.356| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 4271 Z= 0.196 Angle : 0.778 13.494 6011 Z= 0.409 Chirality : 0.047 0.275 711 Planarity : 0.005 0.048 585 Dihedral : 22.643 157.531 1158 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.42 % Allowed : 32.74 % Favored : 62.83 % 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: -0.22 (0.47), residues: 116 sheet: -1.27 (0.63), residues: 78 loop : -2.54 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 674 TYR 0.025 0.002 TYR A 669 PHE 0.012 0.002 PHE A 985 TRP 0.010 0.002 TRP A 745 HIS 0.010 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 ( 4271) covalent geometry : angle 0.77800 / 0.41 ( 6011) hydrogen bonds : bond 0.07890 / 5.37 ( 152) hydrogen bonds : angle 5.55003 / 3.87 ( 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 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8940 (tppp) cc_final: 0.8585 (tppt) REVERT: A 608 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: A 651 MET cc_start: 0.4910 (tpt) cc_final: 0.4618 (tpt) REVERT: A 844 GLU cc_start: 0.2613 (OUTLIER) cc_final: 0.2044 (mp0) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.0757 time to fit residues: 7.0187 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 594 HIS Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 915 VAL 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: 10.0000 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.0770 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.177268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.155778 restraints weight = 12085.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.160378 restraints weight = 7804.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.163695 restraints weight = 5490.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.166152 restraints weight = 4093.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.168037 restraints weight = 3184.203| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4271 Z= 0.172 Angle : 0.803 14.271 6011 Z= 0.408 Chirality : 0.046 0.203 711 Planarity : 0.005 0.047 585 Dihedral : 22.637 158.247 1158 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.83 % Allowed : 34.51 % 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: -2.28 (0.43), residues: 373 helix: -0.24 (0.47), residues: 115 sheet: -1.33 (0.61), residues: 80 loop : -2.50 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 671 TYR 0.038 0.002 TYR A 669 PHE 0.009 0.002 PHE A 985 TRP 0.030 0.002 TRP A 745 HIS 0.005 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 4271) covalent geometry : angle 0.80288 / 0.41 ( 6011) hydrogen bonds : bond 0.06814 / 4.66 ( 152) hydrogen bonds : angle 5.53507 / 3.84 ( 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 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8922 (tppp) cc_final: 0.8584 (tppt) REVERT: A 601 MET cc_start: 0.4646 (tmm) cc_final: 0.4361 (tmm) REVERT: A 651 MET cc_start: 0.5067 (tpt) cc_final: 0.4829 (tpt) REVERT: A 726 ARG cc_start: 0.8146 (mmt180) cc_final: 0.7820 (mmm160) REVERT: A 921 ARG cc_start: 0.8199 (tpm170) cc_final: 0.7797 (ptp-110) outliers start: 13 outliers final: 10 residues processed: 67 average time/residue: 0.0789 time to fit residues: 6.4138 Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 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 849 ASN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 987 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.180570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.159252 restraints weight = 12408.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.163912 restraints weight = 7955.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.167246 restraints weight = 5554.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.169718 restraints weight = 4113.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.171574 restraints weight = 3182.522| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4271 Z= 0.147 Angle : 0.790 15.088 6011 Z= 0.396 Chirality : 0.046 0.236 711 Planarity : 0.005 0.050 585 Dihedral : 22.491 156.696 1158 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.12 % Favored : 90.62 % Rotamer: Outliers : 3.83 % Allowed : 34.81 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.32 (0.43), residues: 373 helix: -0.26 (0.47), residues: 116 sheet: -1.37 (0.60), residues: 80 loop : -2.53 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 671 TYR 0.053 0.002 TYR A 960 PHE 0.017 0.002 PHE A 986 TRP 0.025 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 4271) covalent geometry : angle 0.78959 / 0.40 ( 6011) hydrogen bonds : bond 0.06054 / 4.14 ( 152) hydrogen bonds : angle 5.38109 / 3.72 ( 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 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8905 (tppp) cc_final: 0.8593 (tppt) REVERT: A 601 MET cc_start: 0.4571 (tmm) cc_final: 0.4244 (tmm) REVERT: A 608 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: A 651 MET cc_start: 0.4916 (tpt) cc_final: 0.4693 (tpt) REVERT: A 726 ARG cc_start: 0.8188 (mmt180) cc_final: 0.7853 (tpp-160) REVERT: A 844 GLU cc_start: 0.2608 (OUTLIER) cc_final: 0.2034 (mp0) REVERT: A 921 ARG cc_start: 0.8188 (tpm170) cc_final: 0.7846 (ptp-110) outliers start: 13 outliers final: 10 residues processed: 67 average time/residue: 0.0701 time to fit residues: 5.9198 Evaluate side-chains 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 625 VAL 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 844 GLU Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 915 VAL 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: 0.0020 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 0.0470 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.1490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.175700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.154271 restraints weight = 12243.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.158902 restraints weight = 7801.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.162282 restraints weight = 5466.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.164672 restraints weight = 4052.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.166266 restraints weight = 3147.997| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4271 Z= 0.196 Angle : 0.824 14.247 6011 Z= 0.417 Chirality : 0.047 0.206 711 Planarity : 0.005 0.049 585 Dihedral : 22.584 156.867 1158 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.31 % Favored : 91.42 % Rotamer: Outliers : 4.13 % Allowed : 34.51 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.48), residues: 115 sheet: -1.48 (0.61), residues: 78 loop : -2.55 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 671 TYR 0.046 0.003 TYR A 960 PHE 0.024 0.002 PHE A 986 TRP 0.026 0.003 TRP A 745 HIS 0.006 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 ( 4271) covalent geometry : angle 0.82395 / 0.42 ( 6011) hydrogen bonds : bond 0.07589 / 5.16 ( 152) hydrogen bonds : angle 5.60969 / 3.89 ( 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 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 589 LYS cc_start: 0.8963 (tppp) cc_final: 0.8640 (tppt) REVERT: A 601 MET cc_start: 0.4513 (tmm) cc_final: 0.4277 (tmm) REVERT: A 608 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: A 651 MET cc_start: 0.5304 (tpt) cc_final: 0.5059 (tpt) REVERT: A 683 MET cc_start: -0.0495 (ttt) cc_final: -0.1335 (ptm) REVERT: A 726 ARG cc_start: 0.8273 (mmt180) cc_final: 0.7919 (tpp-160) REVERT: A 844 GLU cc_start: 0.2674 (OUTLIER) cc_final: 0.2085 (mp0) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.0744 time to fit residues: 6.2859 Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 625 VAL 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 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 987 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.177059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.155669 restraints weight = 12248.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.160261 restraints weight = 7792.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.163576 restraints weight = 5489.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.165907 restraints weight = 4105.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.167566 restraints weight = 3191.980| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4271 Z= 0.168 Angle : 0.813 15.166 6011 Z= 0.407 Chirality : 0.046 0.203 711 Planarity : 0.005 0.049 585 Dihedral : 22.570 157.525 1158 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.38 % Favored : 90.35 % Rotamer: Outliers : 3.54 % Allowed : 35.40 % Favored : 61.06 % 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: -0.25 (0.48), residues: 115 sheet: -1.49 (0.60), residues: 78 loop : -2.59 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.031 0.002 TYR A 960 PHE 0.019 0.002 PHE A 986 TRP 0.025 0.002 TRP A 745 HIS 0.003 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 4271) covalent geometry : angle 0.81324 / 0.41 ( 6011) hydrogen bonds : bond 0.06420 / 4.38 ( 152) hydrogen bonds : angle 5.55681 / 3.85 ( 396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 856.57 seconds wall clock time: 15 minutes 30.76 seconds (930.76 seconds total)