Starting phenix.real_space_refine on Sat May 10 08:01:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vu5_43526/05_2025/8vu5_43526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vu5_43526/05_2025/8vu5_43526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vu5_43526/05_2025/8vu5_43526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vu5_43526/05_2025/8vu5_43526.map" model { file = "/net/cci-nas-00/data/ceres_data/8vu5_43526/05_2025/8vu5_43526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vu5_43526/05_2025/8vu5_43526.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 3583 2.51 5 N 968 2.21 5 O 1034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5616 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1119 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "B" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 260} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 264} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.87, per 1000 atoms: 0.69 Number of scatterers: 5616 At special positions: 0 Unit cell: (74.529, 107.289, 93.366, 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 1034 8.00 N 968 7.00 C 3583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 233 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 50 " distance=2.04 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 233 " distance=2.04 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 343 " 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=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 715.6 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 12 sheets defined 17.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 29 through 50 removed outlier: 3.570A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 48 " --> pdb=" O HIS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.681A pdb=" N TRP A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 73 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 105 through 130 removed outlier: 3.508A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.555A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.839A pdb=" N VAL A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 275 through 280 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.599A pdb=" N GLN B 186 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 169 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 268 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 359 Processing sheet with id=AA6, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.723A pdb=" N CYS C 50 " --> pdb=" O CYS C 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.627A pdb=" N HIS C 108 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 123 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 154 removed outlier: 3.641A pdb=" N VAL C 235 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE C 152 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS C 233 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AB1, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AB2, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AB3, first strand: chain 'C' and resid 308 through 310 removed outlier: 3.865A pdb=" N ARG C 308 " --> pdb=" O HIS C 354 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS C 354 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 310 " --> pdb=" O VAL C 352 " (cutoff:3.500A) 137 hydrogen bonds defined for protein. 357 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: 1.32 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1473 1.33 - 1.46: 1536 1.46 - 1.59: 2721 1.59 - 1.72: 0 1.72 - 1.84: 35 Bond restraints: 5765 Sorted by residual: bond pdb=" CA SER A 108 " pdb=" CB SER A 108 " ideal model delta sigma weight residual 1.532 1.475 0.057 1.62e-02 3.81e+03 1.24e+01 bond pdb=" N VAL A 65 " pdb=" CA VAL A 65 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.37e-02 5.33e+03 1.22e+01 bond pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.31e-02 5.83e+03 9.90e+00 bond pdb=" C ASP B 27 " pdb=" N VAL B 28 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.10e-02 8.26e+03 9.10e+00 bond pdb=" N PHE B 41 " pdb=" CA PHE B 41 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.18e-02 7.18e+03 8.60e+00 ... (remaining 5760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 7580 2.00 - 4.00: 221 4.00 - 6.00: 42 6.00 - 8.00: 9 8.00 - 9.99: 1 Bond angle restraints: 7853 Sorted by residual: angle pdb=" N VAL B 28 " pdb=" CA VAL B 28 " pdb=" CB VAL B 28 " ideal model delta sigma weight residual 110.78 100.79 9.99 1.98e+00 2.55e-01 2.55e+01 angle pdb=" CA VAL C 101 " pdb=" C VAL C 101 " pdb=" O VAL C 101 " ideal model delta sigma weight residual 121.59 116.46 5.13 1.03e+00 9.43e-01 2.48e+01 angle pdb=" N PRO B 133 " pdb=" CA PRO B 133 " pdb=" C PRO B 133 " ideal model delta sigma weight residual 111.15 118.88 -7.73 1.58e+00 4.01e-01 2.39e+01 angle pdb=" N SER A 108 " pdb=" CA SER A 108 " pdb=" C SER A 108 " ideal model delta sigma weight residual 112.04 105.08 6.96 1.44e+00 4.82e-01 2.34e+01 angle pdb=" C ASP A 66 " pdb=" N PHE A 67 " pdb=" CA PHE A 67 " ideal model delta sigma weight residual 123.05 116.57 6.48 1.40e+00 5.10e-01 2.14e+01 ... (remaining 7848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2915 17.94 - 35.87: 382 35.87 - 53.81: 123 53.81 - 71.75: 22 71.75 - 89.68: 8 Dihedral angle restraints: 3450 sinusoidal: 1390 harmonic: 2060 Sorted by residual: dihedral pdb=" CB CYS B 326 " pdb=" SG CYS B 326 " pdb=" SG CYS B 343 " pdb=" CB CYS B 343 " ideal model delta sinusoidal sigma weight residual -86.00 -165.85 79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 106 " pdb=" CB CYS A 106 " ideal model delta sinusoidal sigma weight residual 93.00 165.47 -72.47 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS C 326 " pdb=" SG CYS C 326 " pdb=" SG CYS C 343 " pdb=" CB CYS C 343 " ideal model delta sinusoidal sigma weight residual -86.00 -20.83 -65.17 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 3447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 757 0.067 - 0.134: 100 0.134 - 0.200: 11 0.200 - 0.267: 2 0.267 - 0.334: 1 Chirality restraints: 871 Sorted by residual: chirality pdb=" CA VAL B 28 " pdb=" N VAL B 28 " pdb=" C VAL B 28 " pdb=" CB VAL B 28 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA PRO B 133 " pdb=" N PRO B 133 " pdb=" C PRO B 133 " pdb=" CB PRO B 133 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA VAL A 65 " pdb=" N VAL A 65 " pdb=" C VAL A 65 " pdb=" CB VAL A 65 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 868 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 102 " -0.012 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ARG C 102 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG C 102 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 103 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 156 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO C 157 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 64 " 0.012 2.00e-02 2.50e+03 2.25e-02 5.04e+00 pdb=" C ALA A 64 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 64 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 65 " 0.013 2.00e-02 2.50e+03 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 467 2.74 - 3.28: 5516 3.28 - 3.82: 9270 3.82 - 4.36: 10354 4.36 - 4.90: 17653 Nonbonded interactions: 43260 Sorted by model distance: nonbonded pdb=" OG1 THR C 44 " pdb=" OD2 ASP C 47 " model vdw 2.195 3.040 nonbonded pdb=" N PHE C 104 " pdb=" OD2 ASP C 128 " model vdw 2.274 3.120 nonbonded pdb=" O ASP C 128 " pdb=" N ARG C 258 " model vdw 2.290 3.120 nonbonded pdb=" N GLU A 167 " pdb=" OE1 GLU A 167 " model vdw 2.354 3.120 nonbonded pdb=" OE1 GLU C 168 " pdb=" NH2 ARG C 249 " model vdw 2.355 3.120 ... (remaining 43255 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 'B' and (resid 28 through 276 or resid 291 through 292 or resid 295 throu \ gh 319 or (resid 320 and (name N or name CA or name C or name O or name CB )) or \ resid 321 through 326 or resid 341 through 375)) selection = (chain 'C' and (resid 28 through 31 or resid 36 through 53 or resid 64 through 2 \ 78 or resid 295 through 308 or (resid 309 and (name N or name CA or name C or na \ me O or name CB )) or resid 310 through 321 or (resid 322 and (name N or name CA \ or name C or name O or name CB )) or resid 323 through 375)) } 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: 2.100 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.230 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 0.057 5776 Z= 0.310 Angle : 0.811 9.994 7875 Z= 0.479 Chirality : 0.048 0.334 871 Planarity : 0.005 0.058 1011 Dihedral : 17.684 89.682 2079 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.44 % Allowed : 31.14 % Favored : 67.42 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.34), residues: 695 helix: 1.67 (0.54), residues: 107 sheet: -1.16 (0.47), residues: 146 loop : -1.34 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 110 HIS 0.003 0.001 HIS C 153 PHE 0.021 0.002 PHE C 306 TYR 0.021 0.002 TYR C 80 ARG 0.008 0.001 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.24975 ( 137) hydrogen bonds : angle 9.62010 ( 357) SS BOND : bond 0.00563 ( 11) SS BOND : angle 1.61461 ( 22) covalent geometry : bond 0.00515 ( 5765) covalent geometry : angle 0.80745 ( 7853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7506 (p0) cc_final: 0.6231 (p0) REVERT: B 98 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7721 (tp40) REVERT: B 198 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.4868 (t60) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.1600 time to fit residues: 18.1217 Evaluate side-chains 78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 198 TRP Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 0.0040 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 0.0870 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.211144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.169755 restraints weight = 7401.358| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.13 r_work: 0.3808 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5776 Z= 0.126 Angle : 0.640 8.467 7875 Z= 0.323 Chirality : 0.041 0.146 871 Planarity : 0.005 0.057 1011 Dihedral : 6.306 59.913 771 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.98 % Allowed : 26.00 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.34), residues: 695 helix: 1.59 (0.50), residues: 117 sheet: -1.07 (0.42), residues: 171 loop : -1.30 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 110 HIS 0.002 0.000 HIS C 167 PHE 0.019 0.001 PHE B 41 TYR 0.016 0.002 TYR C 80 ARG 0.004 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 137) hydrogen bonds : angle 6.58320 ( 357) SS BOND : bond 0.00451 ( 11) SS BOND : angle 1.58730 ( 22) covalent geometry : bond 0.00277 ( 5765) covalent geometry : angle 0.63578 ( 7853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.6131 (mt0) cc_final: 0.5811 (mm110) REVERT: C 105 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: C 110 TRP cc_start: 0.6875 (p-90) cc_final: 0.6566 (p-90) outliers start: 31 outliers final: 14 residues processed: 101 average time/residue: 0.1728 time to fit residues: 22.9410 Evaluate side-chains 85 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 0.4980 chunk 39 optimal weight: 0.0030 chunk 56 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.0040 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.210930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.169569 restraints weight = 7509.858| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.18 r_work: 0.3797 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5776 Z= 0.117 Angle : 0.594 6.166 7875 Z= 0.296 Chirality : 0.041 0.148 871 Planarity : 0.005 0.055 1011 Dihedral : 5.798 59.159 768 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.33 % Allowed : 27.61 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.35), residues: 695 helix: 1.98 (0.51), residues: 117 sheet: -1.19 (0.40), residues: 181 loop : -1.16 (0.34), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 198 HIS 0.001 0.000 HIS C 167 PHE 0.015 0.001 PHE B 41 TYR 0.009 0.001 TYR C 67 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 137) hydrogen bonds : angle 5.94584 ( 357) SS BOND : bond 0.00366 ( 11) SS BOND : angle 1.40228 ( 22) covalent geometry : bond 0.00262 ( 5765) covalent geometry : angle 0.59054 ( 7853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7158 (mp10) cc_final: 0.6721 (mp10) REVERT: B 26 GLN cc_start: 0.6141 (mt0) cc_final: 0.5838 (mm-40) REVERT: B 149 GLU cc_start: 0.7027 (tp30) cc_final: 0.6666 (mm-30) REVERT: C 105 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: C 110 TRP cc_start: 0.6853 (p-90) cc_final: 0.6576 (p-90) outliers start: 27 outliers final: 12 residues processed: 101 average time/residue: 0.1731 time to fit residues: 23.0839 Evaluate side-chains 83 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.206677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164267 restraints weight = 7534.431| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.49 r_work: 0.3700 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5776 Z= 0.164 Angle : 0.618 6.780 7875 Z= 0.309 Chirality : 0.042 0.152 871 Planarity : 0.005 0.057 1011 Dihedral : 5.652 54.869 766 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.14 % Allowed : 27.45 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.34), residues: 695 helix: 1.80 (0.50), residues: 117 sheet: -1.11 (0.41), residues: 171 loop : -1.23 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 198 HIS 0.001 0.000 HIS C 167 PHE 0.023 0.002 PHE C 105 TYR 0.017 0.002 TYR C 80 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 137) hydrogen bonds : angle 5.92345 ( 357) SS BOND : bond 0.00470 ( 11) SS BOND : angle 1.67978 ( 22) covalent geometry : bond 0.00379 ( 5765) covalent geometry : angle 0.61284 ( 7853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7318 (p0) cc_final: 0.6606 (p0) REVERT: A 78 GLN cc_start: 0.7252 (mp10) cc_final: 0.6825 (mp10) REVERT: B 26 GLN cc_start: 0.6286 (mt0) cc_final: 0.6047 (mm-40) REVERT: B 149 GLU cc_start: 0.7124 (tp30) cc_final: 0.6814 (mm-30) REVERT: C 105 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: C 110 TRP cc_start: 0.7018 (p-90) cc_final: 0.6733 (p-90) outliers start: 32 outliers final: 18 residues processed: 106 average time/residue: 0.1748 time to fit residues: 24.3317 Evaluate side-chains 93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 6.9990 chunk 57 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.207375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165372 restraints weight = 7478.677| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.39 r_work: 0.3725 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5776 Z= 0.143 Angle : 0.603 6.027 7875 Z= 0.301 Chirality : 0.041 0.143 871 Planarity : 0.005 0.057 1011 Dihedral : 5.602 55.919 766 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.14 % Allowed : 27.61 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.34), residues: 695 helix: 1.84 (0.51), residues: 117 sheet: -1.19 (0.40), residues: 176 loop : -1.23 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 198 HIS 0.001 0.000 HIS C 167 PHE 0.023 0.002 PHE C 105 TYR 0.011 0.001 TYR C 69 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 137) hydrogen bonds : angle 5.78431 ( 357) SS BOND : bond 0.00382 ( 11) SS BOND : angle 1.54372 ( 22) covalent geometry : bond 0.00335 ( 5765) covalent geometry : angle 0.59800 ( 7853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7437 (p0) cc_final: 0.6529 (p0) REVERT: A 78 GLN cc_start: 0.7208 (mp10) cc_final: 0.6815 (mp10) REVERT: B 26 GLN cc_start: 0.6303 (mt0) cc_final: 0.6075 (mm-40) REVERT: B 149 GLU cc_start: 0.7101 (tp30) cc_final: 0.6739 (mm-30) REVERT: C 105 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6731 (m-80) REVERT: C 110 TRP cc_start: 0.6982 (p-90) cc_final: 0.6742 (p-90) outliers start: 32 outliers final: 23 residues processed: 103 average time/residue: 0.1849 time to fit residues: 24.5903 Evaluate side-chains 97 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 367 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 0.0980 chunk 42 optimal weight: 0.0010 chunk 65 optimal weight: 6.9990 chunk 57 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.209780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.168420 restraints weight = 7385.398| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.11 r_work: 0.3786 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5776 Z= 0.116 Angle : 0.588 6.022 7875 Z= 0.290 Chirality : 0.041 0.147 871 Planarity : 0.005 0.055 1011 Dihedral : 5.488 56.853 766 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.14 % Allowed : 26.81 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.34), residues: 695 helix: 2.06 (0.51), residues: 117 sheet: -1.15 (0.40), residues: 176 loop : -1.20 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 198 HIS 0.001 0.000 HIS A 142 PHE 0.020 0.001 PHE C 105 TYR 0.018 0.001 TYR C 80 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 137) hydrogen bonds : angle 5.53722 ( 357) SS BOND : bond 0.00458 ( 11) SS BOND : angle 1.43050 ( 22) covalent geometry : bond 0.00264 ( 5765) covalent geometry : angle 0.58422 ( 7853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7301 (p0) cc_final: 0.6450 (p0) REVERT: A 78 GLN cc_start: 0.7196 (mp10) cc_final: 0.6813 (mp10) REVERT: B 26 GLN cc_start: 0.6191 (mt0) cc_final: 0.5954 (mm-40) REVERT: B 149 GLU cc_start: 0.6971 (tp30) cc_final: 0.6560 (mm-30) REVERT: C 105 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6701 (m-80) outliers start: 32 outliers final: 21 residues processed: 106 average time/residue: 0.1733 time to fit residues: 23.8574 Evaluate side-chains 94 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.208140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.166177 restraints weight = 7479.519| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 3.34 r_work: 0.3737 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5776 Z= 0.143 Angle : 0.606 6.142 7875 Z= 0.301 Chirality : 0.042 0.139 871 Planarity : 0.005 0.056 1011 Dihedral : 5.519 56.265 766 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.98 % Allowed : 26.97 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.34), residues: 695 helix: 1.88 (0.50), residues: 117 sheet: -1.15 (0.41), residues: 176 loop : -1.24 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 110 HIS 0.001 0.000 HIS B 167 PHE 0.023 0.002 PHE C 105 TYR 0.017 0.002 TYR C 171 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 137) hydrogen bonds : angle 5.56438 ( 357) SS BOND : bond 0.00430 ( 11) SS BOND : angle 1.41048 ( 22) covalent geometry : bond 0.00333 ( 5765) covalent geometry : angle 0.60270 ( 7853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.593 Fit side-chains REVERT: A 66 ASP cc_start: 0.7560 (p0) cc_final: 0.6661 (p0) REVERT: A 78 GLN cc_start: 0.7241 (mp10) cc_final: 0.6926 (mp10) REVERT: B 26 GLN cc_start: 0.6256 (mt0) cc_final: 0.6008 (mm-40) REVERT: B 149 GLU cc_start: 0.7083 (tp30) cc_final: 0.6719 (mm-30) REVERT: B 257 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6517 (mm) REVERT: C 105 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6730 (m-80) outliers start: 31 outliers final: 23 residues processed: 99 average time/residue: 0.1835 time to fit residues: 23.5964 Evaluate side-chains 96 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.206747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.162757 restraints weight = 7471.462| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 3.20 r_work: 0.3712 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5776 Z= 0.163 Angle : 0.628 6.549 7875 Z= 0.310 Chirality : 0.042 0.141 871 Planarity : 0.005 0.057 1011 Dihedral : 5.601 55.243 766 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.14 % Allowed : 26.97 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.34), residues: 695 helix: 1.77 (0.51), residues: 117 sheet: -1.21 (0.40), residues: 176 loop : -1.28 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 198 HIS 0.002 0.000 HIS B 167 PHE 0.025 0.002 PHE C 105 TYR 0.022 0.002 TYR C 80 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 137) hydrogen bonds : angle 5.64696 ( 357) SS BOND : bond 0.00584 ( 11) SS BOND : angle 1.54226 ( 22) covalent geometry : bond 0.00382 ( 5765) covalent geometry : angle 0.62353 ( 7853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.645 Fit side-chains REVERT: A 66 ASP cc_start: 0.7625 (p0) cc_final: 0.6656 (p0) REVERT: A 78 GLN cc_start: 0.7186 (mp10) cc_final: 0.6827 (mp10) REVERT: B 26 GLN cc_start: 0.6438 (mt0) cc_final: 0.6098 (mm-40) REVERT: B 149 GLU cc_start: 0.7094 (tp30) cc_final: 0.6732 (mm-30) REVERT: B 257 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6617 (mm) REVERT: C 105 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: C 110 TRP cc_start: 0.7080 (p-90) cc_final: 0.6821 (p-90) outliers start: 32 outliers final: 24 residues processed: 99 average time/residue: 0.1820 time to fit residues: 23.3876 Evaluate side-chains 95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.207935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164402 restraints weight = 7452.127| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.21 r_work: 0.3734 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5776 Z= 0.139 Angle : 0.625 7.076 7875 Z= 0.307 Chirality : 0.042 0.146 871 Planarity : 0.005 0.057 1011 Dihedral : 5.580 55.650 766 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.17 % Allowed : 28.09 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.34), residues: 695 helix: 1.91 (0.51), residues: 117 sheet: -1.20 (0.40), residues: 176 loop : -1.28 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 198 HIS 0.002 0.000 HIS B 167 PHE 0.023 0.002 PHE C 105 TYR 0.028 0.002 TYR C 171 ARG 0.003 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 137) hydrogen bonds : angle 5.51234 ( 357) SS BOND : bond 0.00564 ( 11) SS BOND : angle 1.57749 ( 22) covalent geometry : bond 0.00325 ( 5765) covalent geometry : angle 0.62045 ( 7853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.719 Fit side-chains REVERT: A 66 ASP cc_start: 0.7568 (p0) cc_final: 0.6738 (p0) REVERT: A 78 GLN cc_start: 0.7166 (mp10) cc_final: 0.6817 (mp10) REVERT: B 26 GLN cc_start: 0.6419 (mt0) cc_final: 0.6098 (mm-40) REVERT: B 149 GLU cc_start: 0.7079 (tp30) cc_final: 0.6726 (mm-30) REVERT: B 257 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6537 (mm) REVERT: C 105 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: C 110 TRP cc_start: 0.7064 (p-90) cc_final: 0.6794 (p-90) outliers start: 26 outliers final: 22 residues processed: 97 average time/residue: 0.1896 time to fit residues: 24.1536 Evaluate side-chains 94 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.208254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165116 restraints weight = 7500.865| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 3.17 r_work: 0.3745 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5776 Z= 0.134 Angle : 0.624 7.578 7875 Z= 0.306 Chirality : 0.042 0.157 871 Planarity : 0.005 0.056 1011 Dihedral : 5.558 55.577 766 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.17 % Allowed : 28.41 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.34), residues: 695 helix: 2.37 (0.50), residues: 111 sheet: -1.17 (0.41), residues: 171 loop : -1.21 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.002 0.000 HIS B 167 PHE 0.022 0.002 PHE C 105 TYR 0.026 0.002 TYR C 171 ARG 0.003 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 137) hydrogen bonds : angle 5.43990 ( 357) SS BOND : bond 0.00549 ( 11) SS BOND : angle 1.56033 ( 22) covalent geometry : bond 0.00314 ( 5765) covalent geometry : angle 0.61902 ( 7853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.569 Fit side-chains REVERT: A 66 ASP cc_start: 0.7555 (p0) cc_final: 0.6713 (p0) REVERT: A 78 GLN cc_start: 0.7177 (mp10) cc_final: 0.6822 (mp10) REVERT: A 167 GLU cc_start: 0.6878 (mp0) cc_final: 0.6654 (mp0) REVERT: B 26 GLN cc_start: 0.6396 (mt0) cc_final: 0.6145 (mm-40) REVERT: B 149 GLU cc_start: 0.7058 (tp30) cc_final: 0.6680 (mm-30) REVERT: B 257 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6522 (mm) REVERT: C 105 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: C 110 TRP cc_start: 0.7047 (p-90) cc_final: 0.6816 (p-90) outliers start: 26 outliers final: 23 residues processed: 95 average time/residue: 0.1621 time to fit residues: 20.4441 Evaluate side-chains 95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.204866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.162025 restraints weight = 7513.948| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.35 r_work: 0.3680 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5776 Z= 0.191 Angle : 0.663 7.590 7875 Z= 0.328 Chirality : 0.043 0.142 871 Planarity : 0.005 0.058 1011 Dihedral : 5.727 53.999 766 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.17 % Allowed : 28.57 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.34), residues: 695 helix: 2.08 (0.50), residues: 111 sheet: -1.28 (0.40), residues: 174 loop : -1.28 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 198 HIS 0.003 0.001 HIS B 167 PHE 0.033 0.002 PHE C 164 TYR 0.026 0.002 TYR C 171 ARG 0.004 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 137) hydrogen bonds : angle 5.69047 ( 357) SS BOND : bond 0.00557 ( 11) SS BOND : angle 1.60832 ( 22) covalent geometry : bond 0.00450 ( 5765) covalent geometry : angle 0.65892 ( 7853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.27 seconds wall clock time: 55 minutes 52.10 seconds (3352.10 seconds total)