Starting phenix.real_space_refine on Tue Aug 4 16:44:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qp4_53268/08_2026/9qp4_53268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qp4_53268/08_2026/9qp4_53268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qp4_53268/08_2026/9qp4_53268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qp4_53268/08_2026/9qp4_53268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qp4_53268/08_2026/9qp4_53268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qp4_53268/08_2026/9qp4_53268.map" } resolution = 3.06 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= 0.013 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3210 2.51 5 N 804 2.21 5 O 877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4922 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3156 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 2 Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.27, per 1000 atoms: 0.26 Number of scatterers: 4922 At special positions: 0 Unit cell: (64.416, 73.932, 139.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 877 8.00 N 804 7.00 C 3210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 97 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 138.9 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1154 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 53.2% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 29 through 59 removed outlier: 3.802A pdb=" N LEU A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 3.584A pdb=" N TYR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 95 removed outlier: 3.693A pdb=" N TYR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 100 through 135 Processing helix chain 'A' and resid 143 through 163 removed outlier: 4.248A pdb=" N TRP A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 193 through 207 Processing helix chain 'A' and resid 207 through 911 removed outlier: 3.594A pdb=" N ARG A 889 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 934 Processing helix chain 'A' and resid 949 through 972 removed outlier: 3.926A pdb=" N LEU A 969 " --> pdb=" O ASP A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 995 removed outlier: 4.108A pdb=" N ALA A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 272 removed outlier: 3.754A pdb=" N VAL A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Proline residue: A 261 - end of helix removed outlier: 3.975A pdb=" N PHE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 291 through 304 removed outlier: 3.955A pdb=" N ASN A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.876A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.197A pdb=" N PHE L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA2, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.557A pdb=" N SER L 23 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.633A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.613A pdb=" N ILE H 35 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 13 302 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1511 1.34 - 1.46: 1230 1.46 - 1.58: 2269 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 5055 Sorted by residual: bond pdb=" C8 RET A1101 " pdb=" C9 RET A1101 " ideal model delta sigma weight residual 1.450 1.395 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C10 RET A1101 " pdb=" C9 RET A1101 " ideal model delta sigma weight residual 1.359 1.413 -0.054 2.00e-02 2.50e+03 7.30e+00 bond pdb=" N VAL A 227 " pdb=" CA VAL A 227 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.16e+00 bond pdb=" N ASP A 893 " pdb=" CA ASP A 893 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.43e+00 bond pdb=" N LYS A 290 " pdb=" CA LYS A 290 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.31e-02 5.83e+03 5.66e+00 ... (remaining 5050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6674 1.84 - 3.68: 159 3.68 - 5.51: 19 5.51 - 7.35: 3 7.35 - 9.19: 1 Bond angle restraints: 6856 Sorted by residual: angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 116.54 111.34 5.20 1.15e+00 7.56e-01 2.04e+01 angle pdb=" N LYS A 225 " pdb=" CA LYS A 225 " pdb=" C LYS A 225 " ideal model delta sigma weight residual 111.82 108.02 3.80 1.16e+00 7.43e-01 1.08e+01 angle pdb=" N GLU A 895 " pdb=" CA GLU A 895 " pdb=" C GLU A 895 " ideal model delta sigma weight residual 111.36 107.87 3.49 1.09e+00 8.42e-01 1.03e+01 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 110.97 107.55 3.42 1.09e+00 8.42e-01 9.87e+00 angle pdb=" C10 RET A1101 " pdb=" C11 RET A1101 " pdb=" C12 RET A1101 " ideal model delta sigma weight residual 122.68 131.87 -9.19 3.00e+00 1.11e-01 9.38e+00 ... (remaining 6851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2601 17.56 - 35.11: 261 35.11 - 52.67: 60 52.67 - 70.23: 10 70.23 - 87.78: 9 Dihedral angle restraints: 2941 sinusoidal: 1142 harmonic: 1799 Sorted by residual: dihedral pdb=" CD ARG A 889 " pdb=" NE ARG A 889 " pdb=" CZ ARG A 889 " pdb=" NH1 ARG A 889 " ideal model delta sinusoidal sigma weight residual 0.00 -82.35 82.35 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CD ARG A 888 " pdb=" NE ARG A 888 " pdb=" CZ ARG A 888 " pdb=" NH1 ARG A 888 " ideal model delta sinusoidal sigma weight residual 0.00 -77.06 77.06 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -128.09 42.09 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 2938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 531 0.039 - 0.077: 153 0.077 - 0.116: 47 0.116 - 0.154: 12 0.154 - 0.193: 2 Chirality restraints: 745 Sorted by residual: chirality pdb=" CA VAL A 227 " pdb=" N VAL A 227 " pdb=" C VAL A 227 " pdb=" CB VAL A 227 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA ILE L 59 " pdb=" N ILE L 59 " pdb=" C ILE L 59 " pdb=" CB ILE L 59 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 742 not shown) Planarity restraints: 862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 889 " 1.107 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG A 889 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 889 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 889 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 889 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 888 " -1.076 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A 888 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 888 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 888 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 888 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 RET A1101 " 0.135 2.00e-02 2.50e+03 8.17e-02 8.34e+01 pdb=" C11 RET A1101 " -0.099 2.00e-02 2.50e+03 pdb=" C19 RET A1101 " 0.015 2.00e-02 2.50e+03 pdb=" C8 RET A1101 " -0.069 2.00e-02 2.50e+03 pdb=" C9 RET A1101 " 0.018 2.00e-02 2.50e+03 ... (remaining 859 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 2114 2.90 - 3.40: 5139 3.40 - 3.90: 8172 3.90 - 4.40: 9402 4.40 - 4.90: 15216 Nonbonded interactions: 40043 Sorted by model distance: nonbonded pdb=" O GLN A 962 " pdb=" OD1 ASP A 965 " model vdw 2.406 3.040 nonbonded pdb=" O ALA A 926 " pdb=" OD1 ASP A 930 " model vdw 2.455 3.040 nonbonded pdb=" O GLY L 67 " pdb=" OG SER L 68 " model vdw 2.460 3.040 nonbonded pdb=" O ASP A 896 " pdb=" OD1 ASP A 896 " model vdw 2.473 3.040 nonbonded pdb=" O GLY H 9 " pdb=" OE1 GLU H 11 " model vdw 2.490 3.040 ... (remaining 40038 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 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.620 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 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 0.163 5059 Z= 0.327 Angle : 0.672 9.190 6862 Z= 0.412 Chirality : 0.043 0.193 745 Planarity : 0.024 0.496 862 Dihedral : 15.550 87.783 1778 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.09 % Allowed : 17.46 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.19 (0.34), residues: 610 helix: 1.24 (0.31), residues: 293 sheet: -0.96 (0.54), residues: 89 loop : -1.59 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 19 TYR 0.014 0.002 TYR A 217 PHE 0.015 0.001 PHE A 42 TRP 0.015 0.001 TRP A 120 HIS 0.001 0.000 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.23 ( 5055) covalent geometry : angle 0.67210 / 0.41 ( 6856) SS BOND : bond 0.00296 / 0.15 ( 3) SS BOND : angle 0.95457 / 0.47 ( 6) hydrogen bonds : bond 0.12663 / 7.85 ( 297) hydrogen bonds : angle 6.98077 / 5.00 ( 849) Misc. bond : bond 0.16287 / 8.57 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.6092 (pt) cc_final: 0.5870 (pt) REVERT: A 102 HIS cc_start: 0.3939 (OUTLIER) cc_final: 0.3281 (m-70) REVERT: A 247 MET cc_start: 0.4562 (ttp) cc_final: 0.4006 (ttm) REVERT: L 35 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.5206 (m170) outliers start: 11 outliers final: 3 residues processed: 87 average time/residue: 0.0675 time to fit residues: 7.4386 Evaluate side-chains 72 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.279009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.253805 restraints weight = 5594.261| |-----------------------------------------------------------------------------| r_work (start): 0.4826 rms_B_bonded: 2.03 r_work: 0.4399 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5059 Z= 0.144 Angle : 0.613 8.837 6862 Z= 0.322 Chirality : 0.042 0.156 745 Planarity : 0.005 0.036 862 Dihedral : 6.195 84.815 686 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.61 % Allowed : 15.37 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.36 (0.34), residues: 610 helix: 1.69 (0.29), residues: 295 sheet: -0.48 (0.50), residues: 98 loop : -1.46 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 888 TYR 0.016 0.002 TYR L 51 PHE 0.022 0.001 PHE A 42 TRP 0.019 0.001 TRP A 120 HIS 0.001 0.000 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5055) covalent geometry : angle 0.61206 / 0.32 ( 6856) SS BOND : bond 0.00455 / 0.23 ( 3) SS BOND : angle 1.15542 / 0.64 ( 6) hydrogen bonds : bond 0.04173 / 2.71 ( 297) hydrogen bonds : angle 5.01165 / 3.64 ( 849) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6008 (tt) REVERT: A 102 HIS cc_start: 0.3683 (OUTLIER) cc_final: 0.2866 (m-70) REVERT: A 921 LEU cc_start: 0.4654 (OUTLIER) cc_final: 0.4295 (mt) REVERT: L 35 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.4949 (m170) REVERT: H 4 GLN cc_start: 0.6472 (tt0) cc_final: 0.6225 (tt0) outliers start: 19 outliers final: 7 residues processed: 103 average time/residue: 0.0562 time to fit residues: 8.0103 Evaluate side-chains 84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 913 ASN L 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.271513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.210018 restraints weight = 5484.421| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.06 r_work: 0.4176 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 5059 Z= 0.206 Angle : 0.679 7.541 6862 Z= 0.355 Chirality : 0.044 0.154 745 Planarity : 0.005 0.037 862 Dihedral : 6.489 72.860 683 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.74 % Allowed : 15.75 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.48 (0.34), residues: 610 helix: 1.87 (0.30), residues: 294 sheet: -0.48 (0.50), residues: 98 loop : -1.50 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 888 TYR 0.026 0.002 TYR A 130 PHE 0.024 0.002 PHE A 89 TRP 0.020 0.002 TRP A 120 HIS 0.003 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 5055) covalent geometry : angle 0.67804 / 0.35 ( 6856) SS BOND : bond 0.00635 / 0.32 ( 3) SS BOND : angle 1.44838 / 0.80 ( 6) hydrogen bonds : bond 0.04356 / 2.83 ( 297) hydrogen bonds : angle 4.89416 / 3.58 ( 849) Misc. bond : bond 0.00149 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 HIS cc_start: 0.3634 (OUTLIER) cc_final: 0.3032 (m-70) REVERT: A 921 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.4285 (mt) REVERT: A 247 MET cc_start: 0.4103 (ttt) cc_final: 0.2783 (ptt) REVERT: L 35 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.4969 (m170) REVERT: H 4 GLN cc_start: 0.6944 (tt0) cc_final: 0.6663 (tt0) outliers start: 25 outliers final: 17 residues processed: 98 average time/residue: 0.0668 time to fit residues: 8.6931 Evaluate side-chains 93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.269928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4449 r_free = 0.4449 target = 0.211939 restraints weight = 5454.350| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 1.79 r_work: 0.4273 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5059 Z= 0.171 Angle : 0.622 6.599 6862 Z= 0.326 Chirality : 0.042 0.157 745 Planarity : 0.004 0.036 862 Dihedral : 6.461 58.315 683 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.98 % Allowed : 17.65 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.65 (0.34), residues: 610 helix: 1.97 (0.30), residues: 294 sheet: -0.13 (0.51), residues: 98 loop : -1.49 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 889 TYR 0.018 0.002 TYR A 130 PHE 0.013 0.001 PHE H 30 TRP 0.014 0.001 TRP L 36 HIS 0.003 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 5055) covalent geometry : angle 0.62131 / 0.33 ( 6856) SS BOND : bond 0.00548 / 0.28 ( 3) SS BOND : angle 1.29729 / 0.71 ( 6) hydrogen bonds : bond 0.03858 / 2.53 ( 297) hydrogen bonds : angle 4.68678 / 3.43 ( 849) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 HIS cc_start: 0.3509 (OUTLIER) cc_final: 0.2893 (m-70) REVERT: A 921 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.4427 (mt) REVERT: A 247 MET cc_start: 0.4417 (ttt) cc_final: 0.2922 (ptt) REVERT: L 35 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.4670 (m170) outliers start: 21 outliers final: 16 residues processed: 101 average time/residue: 0.0544 time to fit residues: 7.3934 Evaluate side-chains 90 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 53 optimal weight: 0.0370 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.271333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.211860 restraints weight = 5594.633| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 2.11 r_work: 0.4214 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5059 Z= 0.148 Angle : 0.612 7.683 6862 Z= 0.321 Chirality : 0.041 0.142 745 Planarity : 0.004 0.035 862 Dihedral : 6.497 61.558 683 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.50 % Allowed : 16.89 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.81 (0.34), residues: 610 helix: 2.01 (0.30), residues: 296 sheet: 0.22 (0.51), residues: 97 loop : -1.44 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 889 TYR 0.017 0.002 TYR H 103 PHE 0.012 0.001 PHE H 30 TRP 0.033 0.002 TRP A 120 HIS 0.008 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 5055) covalent geometry : angle 0.61084 / 0.32 ( 6856) SS BOND : bond 0.00486 / 0.24 ( 3) SS BOND : angle 1.18598 / 0.65 ( 6) hydrogen bonds : bond 0.03592 / 2.35 ( 297) hydrogen bonds : angle 4.52637 / 3.32 ( 849) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 102 HIS cc_start: 0.3421 (OUTLIER) cc_final: 0.2852 (m-70) REVERT: A 192 TYR cc_start: 0.1855 (m-80) cc_final: 0.1604 (m-80) REVERT: A 921 LEU cc_start: 0.4856 (OUTLIER) cc_final: 0.4375 (mt) REVERT: A 968 LYS cc_start: 0.5126 (pttp) cc_final: 0.4780 (pttp) REVERT: A 247 MET cc_start: 0.4426 (ttp) cc_final: 0.3960 (ttm) REVERT: A 267 MET cc_start: 0.6073 (mmp) cc_final: 0.5861 (mmp) REVERT: L 35 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.4716 (m170) outliers start: 29 outliers final: 20 residues processed: 103 average time/residue: 0.0420 time to fit residues: 6.0042 Evaluate side-chains 97 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 54 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.267212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.215241 restraints weight = 5469.582| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.50 r_work: 0.4281 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5059 Z= 0.169 Angle : 0.633 7.709 6862 Z= 0.332 Chirality : 0.043 0.162 745 Planarity : 0.004 0.035 862 Dihedral : 6.514 60.185 683 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.31 % Allowed : 18.22 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.78 (0.34), residues: 610 helix: 1.98 (0.30), residues: 294 sheet: 0.26 (0.52), residues: 97 loop : -1.45 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.025 0.002 TYR A 130 PHE 0.013 0.001 PHE A 956 TRP 0.044 0.002 TRP A 120 HIS 0.010 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 5055) covalent geometry : angle 0.63239 / 0.33 ( 6856) SS BOND : bond 0.00550 / 0.28 ( 3) SS BOND : angle 1.32574 / 0.72 ( 6) hydrogen bonds : bond 0.03657 / 2.38 ( 297) hydrogen bonds : angle 4.57247 / 3.36 ( 849) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 6 PHE cc_start: 0.5326 (t80) cc_final: 0.4805 (t80) REVERT: A 102 HIS cc_start: 0.3374 (OUTLIER) cc_final: 0.2852 (m-70) REVERT: A 225 LYS cc_start: 0.7714 (pptt) cc_final: 0.7286 (ptmt) REVERT: A 921 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4613 (mt) REVERT: A 968 LYS cc_start: 0.5166 (pttp) cc_final: 0.4788 (pttp) REVERT: A 977 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5162 (mp0) REVERT: A 247 MET cc_start: 0.4490 (ttp) cc_final: 0.3920 (ttm) REVERT: L 35 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.4728 (m170) REVERT: L 74 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5796 (tp) outliers start: 28 outliers final: 22 residues processed: 104 average time/residue: 0.0679 time to fit residues: 9.4394 Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.0000 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 60 optimal weight: 0.1980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.270042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.209591 restraints weight = 5468.286| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.05 r_work: 0.4211 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5059 Z= 0.147 Angle : 0.609 8.430 6862 Z= 0.320 Chirality : 0.042 0.143 745 Planarity : 0.004 0.035 862 Dihedral : 6.420 63.102 683 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.31 % Allowed : 18.60 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.91 (0.35), residues: 610 helix: 1.99 (0.30), residues: 297 sheet: 0.39 (0.51), residues: 97 loop : -1.33 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.021 0.002 TYR A 130 PHE 0.037 0.001 PHE A 89 TRP 0.041 0.002 TRP A 120 HIS 0.008 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 5055) covalent geometry : angle 0.60825 / 0.32 ( 6856) SS BOND : bond 0.00487 / 0.24 ( 3) SS BOND : angle 1.16603 / 0.63 ( 6) hydrogen bonds : bond 0.03488 / 2.29 ( 297) hydrogen bonds : angle 4.45574 / 3.27 ( 849) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 6 PHE cc_start: 0.5451 (t80) cc_final: 0.4948 (t80) REVERT: A 102 HIS cc_start: 0.3442 (OUTLIER) cc_final: 0.2701 (m-70) REVERT: A 192 TYR cc_start: 0.1879 (m-80) cc_final: 0.1671 (m-80) REVERT: A 225 LYS cc_start: 0.7698 (pptt) cc_final: 0.7299 (ptmt) REVERT: A 921 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4674 (mt) REVERT: A 968 LYS cc_start: 0.5426 (pttp) cc_final: 0.4879 (pttp) REVERT: A 977 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5496 (mp0) REVERT: A 994 GLN cc_start: 0.6280 (mm-40) cc_final: 0.5762 (mt0) REVERT: L 35 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.4681 (m170) REVERT: L 74 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5675 (tp) outliers start: 28 outliers final: 22 residues processed: 99 average time/residue: 0.0550 time to fit residues: 7.5517 Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 979 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.260443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.197444 restraints weight = 5479.837| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 1.88 r_work: 0.4110 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 5059 Z= 0.283 Angle : 0.758 7.694 6862 Z= 0.400 Chirality : 0.047 0.169 745 Planarity : 0.005 0.037 862 Dihedral : 6.936 62.699 683 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.83 % Allowed : 17.65 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.21 (0.34), residues: 610 helix: 1.56 (0.30), residues: 297 sheet: -0.25 (0.54), residues: 89 loop : -1.68 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 46 TYR 0.026 0.003 TYR H 104 PHE 0.055 0.002 PHE A 89 TRP 0.049 0.003 TRP A 120 HIS 0.008 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 ( 5055) covalent geometry : angle 0.75640 / 0.40 ( 6856) SS BOND : bond 0.00853 / 0.42 ( 3) SS BOND : angle 1.83456 / 0.99 ( 6) hydrogen bonds : bond 0.04414 / 2.84 ( 297) hydrogen bonds : angle 5.11625 / 3.77 ( 849) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.114 Fit side-chains REVERT: A 6 PHE cc_start: 0.5539 (t80) cc_final: 0.4996 (t80) REVERT: A 49 ASN cc_start: 0.5353 (t0) cc_final: 0.4573 (t0) REVERT: A 102 HIS cc_start: 0.3271 (OUTLIER) cc_final: 0.2813 (m-70) REVERT: A 225 LYS cc_start: 0.7758 (pptt) cc_final: 0.7365 (ptmt) REVERT: A 921 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5153 (mt) REVERT: A 977 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: A 994 GLN cc_start: 0.6507 (mm-40) cc_final: 0.5940 (mt0) REVERT: A 247 MET cc_start: 0.4200 (ttt) cc_final: 0.3220 (mtp) REVERT: A 296 ASN cc_start: 0.7428 (t0) cc_final: 0.6600 (m-40) REVERT: L 35 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.5340 (m170) REVERT: L 43 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.5724 (pp20) REVERT: L 74 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.5923 (tp) outliers start: 36 outliers final: 29 residues processed: 102 average time/residue: 0.0427 time to fit residues: 6.2344 Evaluate side-chains 106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.264002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.205582 restraints weight = 5403.456| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 1.90 r_work: 0.4178 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5059 Z= 0.218 Angle : 0.676 7.763 6862 Z= 0.357 Chirality : 0.044 0.163 745 Planarity : 0.004 0.036 862 Dihedral : 6.751 62.359 683 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.64 % Allowed : 17.65 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.21 (0.34), residues: 610 helix: 1.56 (0.31), residues: 294 sheet: -0.11 (0.55), residues: 88 loop : -1.69 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.021 0.002 TYR H 104 PHE 0.032 0.002 PHE A 89 TRP 0.036 0.002 TRP A 120 HIS 0.008 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 ( 5055) covalent geometry : angle 0.67451 / 0.36 ( 6856) SS BOND : bond 0.00650 / 0.33 ( 3) SS BOND : angle 1.50027 / 0.80 ( 6) hydrogen bonds : bond 0.03988 / 2.54 ( 297) hydrogen bonds : angle 4.93337 / 3.65 ( 849) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.183 Fit side-chains REVERT: A 6 PHE cc_start: 0.5362 (t80) cc_final: 0.4846 (t80) REVERT: A 49 ASN cc_start: 0.5297 (t0) cc_final: 0.4601 (t0) REVERT: A 102 HIS cc_start: 0.3223 (OUTLIER) cc_final: 0.2647 (m-70) REVERT: A 225 LYS cc_start: 0.7795 (pptt) cc_final: 0.7452 (ptmt) REVERT: A 921 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5381 (mt) REVERT: A 968 LYS cc_start: 0.5427 (pttp) cc_final: 0.5051 (pttp) REVERT: A 994 GLN cc_start: 0.6558 (mm-40) cc_final: 0.6077 (mt0) REVERT: A 296 ASN cc_start: 0.7410 (t0) cc_final: 0.6615 (m-40) REVERT: A 303 MET cc_start: 0.4435 (mtt) cc_final: 0.3437 (ppp) REVERT: L 35 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.4791 (m170) REVERT: L 74 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.5740 (tp) outliers start: 35 outliers final: 27 residues processed: 102 average time/residue: 0.0589 time to fit residues: 8.3092 Evaluate side-chains 101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 60 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.5243 > 50:) chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.266136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.208097 restraints weight = 5463.961| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 1.94 r_work: 0.4227 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5059 Z= 0.168 Angle : 0.633 7.162 6862 Z= 0.333 Chirality : 0.042 0.145 745 Planarity : 0.004 0.036 862 Dihedral : 6.570 62.399 683 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.26 % Allowed : 17.27 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.44 (0.34), residues: 610 helix: 1.64 (0.30), residues: 296 sheet: 0.12 (0.52), residues: 98 loop : -1.57 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.020 0.002 TYR A 130 PHE 0.016 0.001 PHE A 89 TRP 0.030 0.002 TRP A 120 HIS 0.008 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 5055) covalent geometry : angle 0.63200 / 0.33 ( 6856) SS BOND : bond 0.00527 / 0.27 ( 3) SS BOND : angle 1.24304 / 0.67 ( 6) hydrogen bonds : bond 0.03638 / 2.33 ( 297) hydrogen bonds : angle 4.68013 / 3.43 ( 849) Misc. bond : bond 0.00032 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.241 Fit side-chains REVERT: A 6 PHE cc_start: 0.5538 (t80) cc_final: 0.5008 (t80) REVERT: A 49 ASN cc_start: 0.5464 (t0) cc_final: 0.4742 (t0) REVERT: A 102 HIS cc_start: 0.3039 (OUTLIER) cc_final: 0.2494 (m-70) REVERT: A 225 LYS cc_start: 0.7775 (pptt) cc_final: 0.7433 (ptmt) REVERT: A 921 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5297 (mt) REVERT: A 968 LYS cc_start: 0.5417 (pttp) cc_final: 0.5028 (pttp) REVERT: A 994 GLN cc_start: 0.6506 (mm-40) cc_final: 0.5979 (mt0) REVERT: A 247 MET cc_start: 0.4641 (ptt) cc_final: 0.3325 (ttp) REVERT: A 267 MET cc_start: 0.5512 (mmp) cc_final: 0.5180 (mmp) REVERT: A 296 ASN cc_start: 0.7396 (t0) cc_final: 0.6595 (m-40) REVERT: L 35 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.4823 (m170) REVERT: L 74 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5724 (tp) outliers start: 33 outliers final: 25 residues processed: 94 average time/residue: 0.0671 time to fit residues: 8.7287 Evaluate side-chains 96 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.264281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.204073 restraints weight = 5437.059| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.86 r_work: 0.4207 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 5059 Z= 0.203 Angle : 0.670 7.305 6862 Z= 0.352 Chirality : 0.044 0.167 745 Planarity : 0.004 0.036 862 Dihedral : 6.645 64.032 683 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.69 % Allowed : 17.84 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.39 (0.34), residues: 610 helix: 1.68 (0.31), residues: 296 sheet: -0.15 (0.52), residues: 99 loop : -1.59 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.018 0.002 TYR L 51 PHE 0.016 0.001 PHE A 956 TRP 0.034 0.002 TRP A 120 HIS 0.009 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 5055) covalent geometry : angle 0.66915 / 0.35 ( 6856) SS BOND : bond 0.00619 / 0.31 ( 3) SS BOND : angle 1.37031 / 0.74 ( 6) hydrogen bonds : bond 0.03775 / 2.42 ( 297) hydrogen bonds : angle 4.74306 / 3.50 ( 849) Misc. bond : bond 0.00037 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.44 seconds wall clock time: 28 minutes 32.34 seconds (1712.34 seconds total)