Starting phenix.real_space_refine on Thu Sep 18 10:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwf_47242/09_2025/9dwf_47242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwf_47242/09_2025/9dwf_47242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwf_47242/09_2025/9dwf_47242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwf_47242/09_2025/9dwf_47242.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwf_47242/09_2025/9dwf_47242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwf_47242/09_2025/9dwf_47242.cif" } resolution = 3.1 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5752 atoms to isotropic. 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 293 5.49 5 S 10 5.16 5 C 6598 2.51 5 N 2239 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11949 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2383 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 28} Time building chain proxies: 3.10, per 1000 atoms: 0.26 Number of scatterers: 11949 At special positions: 0 Unit cell: (73.927, 124.313, 118.531, 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 10 16.00 P 293 15.00 O 2809 8.00 N 2239 7.00 C 6598 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: 0.98 Conformation dependent library (CDL) restraints added in 464.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 72.8% alpha, 2.7% beta 145 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.576A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.222A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.514A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.358A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.690A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.535A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 42 through 57 removed outlier: 4.132A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.611A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.676A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.638A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.589A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.381A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.721A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.519A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.767A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.313A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.546A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.439A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.128A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.137A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 390 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 742 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2192 1.33 - 1.45: 4201 1.45 - 1.57: 5761 1.57 - 1.69: 585 1.69 - 1.81: 20 Bond restraints: 12759 Sorted by residual: bond pdb=" P DC K 119 " pdb=" OP3 DC K 119 " ideal model delta sigma weight residual 1.480 1.608 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.74e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.54e-02 4.22e+03 5.14e+00 bond pdb=" P DA K 120 " pdb=" OP2 DA K 120 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.30e+00 ... (remaining 12754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 18424 3.05 - 6.09: 50 6.09 - 9.14: 13 9.14 - 12.19: 0 12.19 - 15.23: 1 Bond angle restraints: 18488 Sorted by residual: angle pdb=" O3' DA K 120 " pdb=" C3' DA K 120 " pdb=" C2' DA K 120 " ideal model delta sigma weight residual 111.50 96.27 15.23 1.50e+00 4.44e-01 1.03e+02 angle pdb=" C LYS C 74 " pdb=" N LYS C 75 " pdb=" CA LYS C 75 " ideal model delta sigma weight residual 122.94 116.30 6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" C4' DA K 120 " pdb=" C3' DA K 120 " pdb=" O3' DA K 120 " ideal model delta sigma weight residual 110.00 103.81 6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " pdb=" CG ASP F 24 " ideal model delta sigma weight residual 112.60 116.22 -3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" N GLY G 37 " pdb=" CA GLY G 37 " pdb=" C GLY G 37 " ideal model delta sigma weight residual 113.27 117.93 -4.66 1.33e+00 5.65e-01 1.23e+01 ... (remaining 18483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 5124 28.10 - 56.20: 1615 56.20 - 84.30: 171 84.30 - 112.40: 0 112.40 - 140.49: 3 Dihedral angle restraints: 6913 sinusoidal: 4744 harmonic: 2169 Sorted by residual: dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DG J 82 " pdb=" C3' DG J 82 " pdb=" O3' DG J 82 " pdb=" P DT J 83 " ideal model delta sinusoidal sigma weight residual 220.00 79.51 140.49 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 80.10 139.90 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2094 0.131 - 0.262: 8 0.262 - 0.392: 0 0.392 - 0.523: 0 0.523 - 0.654: 3 Chirality restraints: 2105 Sorted by residual: chirality pdb=" P DC K 119 " pdb=" OP1 DC K 119 " pdb=" OP2 DC K 119 " pdb=" O5' DC K 119 " both_signs ideal model delta sigma weight residual True 2.35 3.00 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DA K 120 " pdb=" OP1 DA K 120 " pdb=" OP2 DA K 120 " pdb=" O5' DA K 120 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" P DG J 29 " pdb=" OP1 DG J 29 " pdb=" OP2 DG J 29 " pdb=" O5' DG J 29 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.83e+00 ... (remaining 2102 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 116 " -0.050 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO C 117 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 50 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLU A 50 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 50 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 51 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 23 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARG B 23 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG B 23 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP B 24 " -0.013 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1685 2.76 - 3.30: 9962 3.30 - 3.83: 23782 3.83 - 4.37: 27984 4.37 - 4.90: 39584 Nonbonded interactions: 102997 Sorted by model distance: nonbonded pdb=" O ARG F 23 " pdb=" OD1 ASP F 24 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.335 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.369 3.040 nonbonded pdb=" N ALA A 47 " pdb=" OP2 DT J 83 " model vdw 2.387 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.408 3.040 ... (remaining 102992 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } 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 individual isotropic 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: 18.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.004 0.128 12759 Z= 0.183 Angle : 0.625 15.235 18488 Z= 0.369 Chirality : 0.042 0.654 2105 Planarity : 0.005 0.074 1322 Dihedral : 27.534 140.495 5515 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 aren not related in a simple way. whole: 1.00 (0.30), residues: 733 helix: 1.29 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.022 0.002 TYR H 40 PHE 0.012 0.002 PHE H 70 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00386 (12759) covalent geometry : angle 0.62472 (18488) hydrogen bonds : bond 0.13342 ( 761) hydrogen bonds : angle 4.26418 ( 1900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.277 Fit side-chains REVERT: B 91 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8237 (ttpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1641 time to fit residues: 33.4444 Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095115 restraints weight = 18366.023| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.03 r_work: 0.2994 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12759 Z= 0.254 Angle : 0.602 5.511 18488 Z= 0.356 Chirality : 0.037 0.170 2105 Planarity : 0.005 0.036 1322 Dihedral : 30.626 141.497 4034 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.25 % Allowed : 6.42 % Favored : 91.33 % 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 aren not related in a simple way. whole: 1.55 (0.31), residues: 733 helix: 1.68 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.020 0.002 TYR D 40 PHE 0.013 0.002 PHE C 25 HIS 0.004 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00581 (12759) covalent geometry : angle 0.60179 (18488) hydrogen bonds : bond 0.04991 ( 761) hydrogen bonds : angle 3.11153 ( 1900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.313 Fit side-chains REVERT: C 73 ASN cc_start: 0.8183 (t0) cc_final: 0.7913 (t0) REVERT: H 113 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7672 (mm-30) REVERT: H 116 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8767 (ttpt) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.1465 time to fit residues: 25.6482 Evaluate side-chains 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096916 restraints weight = 18611.027| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.04 r_work: 0.3028 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12759 Z= 0.159 Angle : 0.542 5.335 18488 Z= 0.328 Chirality : 0.034 0.145 2105 Planarity : 0.004 0.035 1322 Dihedral : 30.595 141.177 4034 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.61 % Allowed : 8.51 % Favored : 89.89 % 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 aren not related in a simple way. whole: 2.06 (0.30), residues: 733 helix: 2.09 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.71 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.017 0.001 TYR D 40 PHE 0.008 0.001 PHE E 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00343 (12759) covalent geometry : angle 0.54234 (18488) hydrogen bonds : bond 0.04022 ( 761) hydrogen bonds : angle 2.93288 ( 1900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.377 Fit side-chains REVERT: C 73 ASN cc_start: 0.8218 (t0) cc_final: 0.7990 (t0) REVERT: H 57 LYS cc_start: 0.8689 (mttt) cc_final: 0.8450 (mtpp) outliers start: 10 outliers final: 10 residues processed: 134 average time/residue: 0.1525 time to fit residues: 27.2112 Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.3893 r_free = 0.3893 target = 0.141650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098801 restraints weight = 18537.253| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.03 r_work: 0.3061 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12759 Z= 0.144 Angle : 0.512 5.181 18488 Z= 0.315 Chirality : 0.032 0.150 2105 Planarity : 0.004 0.034 1322 Dihedral : 30.436 140.043 4034 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.09 % Allowed : 8.35 % Favored : 89.57 % 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 aren not related in a simple way. whole: 2.49 (0.31), residues: 733 helix: 2.34 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.51 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.016 0.001 TYR D 40 PHE 0.007 0.001 PHE D 70 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00306 (12759) covalent geometry : angle 0.51206 (18488) hydrogen bonds : bond 0.03432 ( 761) hydrogen bonds : angle 2.73565 ( 1900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.395 Fit side-chains REVERT: C 73 ASN cc_start: 0.8190 (t0) cc_final: 0.7850 (t0) REVERT: H 57 LYS cc_start: 0.8594 (mttt) cc_final: 0.8390 (mtpp) REVERT: H 116 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8584 (ttpt) outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 0.1488 time to fit residues: 28.1112 Evaluate side-chains 138 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095612 restraints weight = 18380.922| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.03 r_work: 0.3003 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12759 Z= 0.214 Angle : 0.564 5.269 18488 Z= 0.338 Chirality : 0.035 0.159 2105 Planarity : 0.004 0.042 1322 Dihedral : 30.607 139.828 4034 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.09 % Allowed : 9.95 % Favored : 87.96 % 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 aren not related in a simple way. whole: 2.29 (0.31), residues: 733 helix: 2.31 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.014 0.002 TYR D 40 PHE 0.010 0.002 PHE C 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00486 (12759) covalent geometry : angle 0.56368 (18488) hydrogen bonds : bond 0.04355 ( 761) hydrogen bonds : angle 2.87133 ( 1900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.274 Fit side-chains REVERT: C 73 ASN cc_start: 0.8249 (t0) cc_final: 0.7897 (t0) REVERT: H 57 LYS cc_start: 0.8723 (mttt) cc_final: 0.8500 (mtpp) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.1439 time to fit residues: 25.1713 Evaluate side-chains 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.3874 r_free = 0.3874 target = 0.140196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097049 restraints weight = 18320.709| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.03 r_work: 0.3028 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12759 Z= 0.149 Angle : 0.533 5.207 18488 Z= 0.325 Chirality : 0.033 0.141 2105 Planarity : 0.004 0.039 1322 Dihedral : 30.622 140.296 4034 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.77 % Allowed : 10.11 % Favored : 88.12 % 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 aren not related in a simple way. whole: 2.46 (0.31), residues: 733 helix: 2.43 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.66 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.014 0.001 TYR D 40 PHE 0.007 0.001 PHE D 70 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00318 (12759) covalent geometry : angle 0.53344 (18488) hydrogen bonds : bond 0.03871 ( 761) hydrogen bonds : angle 2.81124 ( 1900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.348 Fit side-chains REVERT: C 73 ASN cc_start: 0.8239 (t0) cc_final: 0.7900 (t0) REVERT: H 57 LYS cc_start: 0.8676 (mttt) cc_final: 0.8468 (mtpp) outliers start: 11 outliers final: 11 residues processed: 134 average time/residue: 0.1409 time to fit residues: 25.2766 Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.3870 r_free = 0.3870 target = 0.139970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096780 restraints weight = 18477.627| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.02 r_work: 0.3023 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12759 Z= 0.172 Angle : 0.533 5.202 18488 Z= 0.324 Chirality : 0.033 0.145 2105 Planarity : 0.004 0.042 1322 Dihedral : 30.580 139.792 4034 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.61 % Allowed : 11.08 % Favored : 87.32 % 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 aren not related in a simple way. whole: 2.49 (0.31), residues: 733 helix: 2.45 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.013 0.001 TYR D 40 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00382 (12759) covalent geometry : angle 0.53262 (18488) hydrogen bonds : bond 0.03819 ( 761) hydrogen bonds : angle 2.78069 ( 1900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.345 Fit side-chains REVERT: C 73 ASN cc_start: 0.8225 (t0) cc_final: 0.7876 (t0) outliers start: 10 outliers final: 10 residues processed: 131 average time/residue: 0.1459 time to fit residues: 25.5643 Evaluate side-chains 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.3877 r_free = 0.3877 target = 0.140455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097291 restraints weight = 18265.206| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.03 r_work: 0.3036 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12759 Z= 0.149 Angle : 0.525 5.200 18488 Z= 0.321 Chirality : 0.033 0.147 2105 Planarity : 0.004 0.041 1322 Dihedral : 30.584 139.807 4034 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 11.72 % Favored : 86.68 % 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 aren not related in a simple way. whole: 2.59 (0.31), residues: 733 helix: 2.51 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.56 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.013 0.001 TYR D 40 PHE 0.006 0.001 PHE E 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00318 (12759) covalent geometry : angle 0.52507 (18488) hydrogen bonds : bond 0.03672 ( 761) hydrogen bonds : angle 2.76774 ( 1900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.301 Fit side-chains REVERT: C 73 ASN cc_start: 0.8222 (t0) cc_final: 0.7869 (t0) outliers start: 10 outliers final: 10 residues processed: 135 average time/residue: 0.1506 time to fit residues: 26.9910 Evaluate side-chains 135 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.3862 r_free = 0.3862 target = 0.139330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095929 restraints weight = 18316.114| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.03 r_work: 0.3011 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12759 Z= 0.197 Angle : 0.547 5.288 18488 Z= 0.331 Chirality : 0.034 0.151 2105 Planarity : 0.004 0.045 1322 Dihedral : 30.630 139.524 4034 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.61 % Allowed : 12.20 % Favored : 86.20 % 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 aren not related in a simple way. whole: 2.44 (0.31), residues: 733 helix: 2.41 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.013 0.002 TYR D 40 PHE 0.009 0.002 PHE E 84 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00443 (12759) covalent geometry : angle 0.54694 (18488) hydrogen bonds : bond 0.04123 ( 761) hydrogen bonds : angle 2.80486 ( 1900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.224 Fit side-chains REVERT: C 73 ASN cc_start: 0.8245 (t0) cc_final: 0.7904 (t0) REVERT: H 113 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7863 (mm-30) outliers start: 10 outliers final: 9 residues processed: 126 average time/residue: 0.1436 time to fit residues: 23.8427 Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 0.0040 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 0.0470 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** 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 = 0.3874 r_free = 0.3874 target = 0.140275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097132 restraints weight = 18379.919| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.03 r_work: 0.3034 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12759 Z= 0.145 Angle : 0.533 5.177 18488 Z= 0.326 Chirality : 0.033 0.162 2105 Planarity : 0.004 0.045 1322 Dihedral : 30.642 140.197 4034 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.44 % Allowed : 12.36 % Favored : 86.20 % 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 aren not related in a simple way. whole: 2.65 (0.31), residues: 733 helix: 2.54 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.55 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.015 0.001 TYR D 40 PHE 0.005 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00304 (12759) covalent geometry : angle 0.53313 (18488) hydrogen bonds : bond 0.03706 ( 761) hydrogen bonds : angle 2.76708 ( 1900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.364 Fit side-chains REVERT: C 73 ASN cc_start: 0.8219 (t0) cc_final: 0.7879 (t0) outliers start: 9 outliers final: 9 residues processed: 134 average time/residue: 0.1507 time to fit residues: 26.8498 Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.3868 r_free = 0.3868 target = 0.139848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096643 restraints weight = 18287.660| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.02 r_work: 0.3023 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12759 Z= 0.176 Angle : 0.537 5.217 18488 Z= 0.326 Chirality : 0.033 0.142 2105 Planarity : 0.004 0.045 1322 Dihedral : 30.605 139.658 4034 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.28 % Allowed : 13.00 % Favored : 85.71 % 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 aren not related in a simple way. whole: 2.57 (0.31), residues: 733 helix: 2.50 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.013 0.001 TYR D 40 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00392 (12759) covalent geometry : angle 0.53693 (18488) hydrogen bonds : bond 0.03827 ( 761) hydrogen bonds : angle 2.75703 ( 1900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4275.55 seconds wall clock time: 73 minutes 29.51 seconds (4409.51 seconds total)