Starting phenix.real_space_refine on Sun Apr 27 12:01:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vu5_43526/04_2025/8vu5_43526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vu5_43526/04_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_43526/04_2025/8vu5_43526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vu5_43526/04_2025/8vu5_43526.map" model { file = "/net/cci-nas-00/data/ceres_data/8vu5_43526/04_2025/8vu5_43526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vu5_43526/04_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-5669/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: 4.38, per 1000 atoms: 0.78 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: 1.37 Conformation dependent library (CDL) restraints added in 742.8 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: 0.63 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: 1.31 Time building geometry restraints manager: 1.64 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: 27.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.530 ------------------------------------------------------------------------------- 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 : 0.610 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: 0.1746 time to fit residues: 19.8624 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 : 0.637 ------------------------------------------------------------------------------- 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 = 0.169756 restraints weight = 7401.359| |-----------------------------------------------------------------------------| 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: 0.7049 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 : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.6138 (mt0) cc_final: 0.5813 (mm110) REVERT: C 105 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: C 110 TRP cc_start: 0.6873 (p-90) cc_final: 0.6565 (p-90) outliers start: 31 outliers final: 14 residues processed: 101 average time/residue: 0.1860 time to fit residues: 24.6824 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 : 0.630 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.205637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162751 restraints weight = 7522.380| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.34 r_work: 0.3699 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5776 Z= 0.173 Angle : 0.633 6.503 7875 Z= 0.318 Chirality : 0.042 0.144 871 Planarity : 0.005 0.058 1011 Dihedral : 5.935 55.679 768 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.82 % Allowed : 26.65 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.11 (0.34), residues: 695 helix: 1.68 (0.50), residues: 117 sheet: -1.12 (0.42), residues: 171 loop : -1.31 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 198 HIS 0.002 0.001 HIS A 44 PHE 0.021 0.002 PHE C 105 TYR 0.015 0.002 TYR C 69 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 137) hydrogen bonds : angle 6.25082 ( 357) SS BOND : bond 0.00475 ( 11) SS BOND : angle 1.45108 ( 22) covalent geometry : bond 0.00402 ( 5765) covalent geometry : angle 0.62928 ( 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 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7267 (p0) cc_final: 0.6673 (p0) REVERT: A 78 GLN cc_start: 0.7251 (mp10) cc_final: 0.6941 (mp10) REVERT: A 163 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6831 (tt) REVERT: B 26 GLN cc_start: 0.6378 (mt0) cc_final: 0.6048 (mm-40) REVERT: B 149 GLU cc_start: 0.7153 (tp30) cc_final: 0.6867 (mm-30) REVERT: C 105 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: C 110 TRP cc_start: 0.7012 (p-90) cc_final: 0.6783 (p-90) REVERT: C 233 CYS cc_start: 0.6589 (t) cc_final: 0.6231 (t) outliers start: 30 outliers final: 15 residues processed: 105 average time/residue: 0.1711 time to fit residues: 23.4546 Evaluate side-chains 87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 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 145 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 26 optimal weight: 0.0020 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.4502 r_free = 0.4502 target = 0.208770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166548 restraints weight = 7477.410| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.21 r_work: 0.3758 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5776 Z= 0.127 Angle : 0.630 7.620 7875 Z= 0.311 Chirality : 0.041 0.150 871 Planarity : 0.005 0.057 1011 Dihedral : 5.599 56.696 766 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.82 % Allowed : 26.81 % Favored : 68.38 % 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: 1.84 (0.50), residues: 117 sheet: -1.16 (0.41), residues: 171 loop : -1.29 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 198 HIS 0.001 0.000 HIS C 153 PHE 0.020 0.001 PHE C 105 TYR 0.018 0.001 TYR C 80 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 137) hydrogen bonds : angle 5.86867 ( 357) SS BOND : bond 0.00478 ( 11) SS BOND : angle 2.23316 ( 22) covalent geometry : bond 0.00293 ( 5765) covalent geometry : angle 0.62017 ( 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 103 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7177 (p0) cc_final: 0.6360 (p0) REVERT: A 78 GLN cc_start: 0.7171 (mp10) cc_final: 0.6775 (mp10) REVERT: B 26 GLN cc_start: 0.6274 (mt0) cc_final: 0.5956 (mm-40) REVERT: B 149 GLU cc_start: 0.7079 (tp30) cc_final: 0.6729 (mm-30) REVERT: C 105 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: C 110 TRP cc_start: 0.6923 (p-90) cc_final: 0.6662 (p-90) outliers start: 30 outliers final: 17 residues processed: 100 average time/residue: 0.1722 time to fit residues: 22.5775 Evaluate side-chains 87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 B residue 355 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4475 r_free = 0.4475 target = 0.206074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163422 restraints weight = 7441.321| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.32 r_work: 0.3700 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5776 Z= 0.166 Angle : 0.644 6.501 7875 Z= 0.319 Chirality : 0.042 0.147 871 Planarity : 0.005 0.059 1011 Dihedral : 5.657 54.078 766 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.78 % Allowed : 26.48 % 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: -1.16 (0.34), residues: 695 helix: 1.77 (0.50), residues: 117 sheet: -1.25 (0.40), residues: 176 loop : -1.33 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 198 HIS 0.002 0.001 HIS C 367 PHE 0.025 0.002 PHE C 105 TYR 0.014 0.002 TYR C 69 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 137) hydrogen bonds : angle 5.91163 ( 357) SS BOND : bond 0.00463 ( 11) SS BOND : angle 2.05293 ( 22) covalent geometry : bond 0.00389 ( 5765) covalent geometry : angle 0.63542 ( 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 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7653 (p0) cc_final: 0.6865 (p0) REVERT: A 78 GLN cc_start: 0.7221 (mp10) cc_final: 0.6894 (mp10) REVERT: B 26 GLN cc_start: 0.6443 (mt0) cc_final: 0.6185 (mm-40) REVERT: B 149 GLU cc_start: 0.7118 (tp30) cc_final: 0.6819 (mm-30) REVERT: B 257 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6607 (mm) REVERT: C 105 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: C 110 TRP cc_start: 0.7081 (p-90) cc_final: 0.6783 (p-90) outliers start: 36 outliers final: 23 residues processed: 104 average time/residue: 0.2190 time to fit residues: 29.8313 Evaluate side-chains 93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 184 VAL 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 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 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: 1.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.204544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.161682 restraints weight = 7403.202| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.35 r_work: 0.3671 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5776 Z= 0.187 Angle : 0.649 8.918 7875 Z= 0.320 Chirality : 0.043 0.142 871 Planarity : 0.005 0.060 1011 Dihedral : 5.760 55.369 766 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.62 % Allowed : 27.13 % 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: -1.23 (0.34), residues: 695 helix: 1.60 (0.50), residues: 117 sheet: -1.30 (0.40), residues: 174 loop : -1.34 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 198 HIS 0.002 0.001 HIS B 167 PHE 0.027 0.002 PHE C 105 TYR 0.020 0.002 TYR C 80 ARG 0.004 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 137) hydrogen bonds : angle 5.95602 ( 357) SS BOND : bond 0.00523 ( 11) SS BOND : angle 1.78001 ( 22) covalent geometry : bond 0.00440 ( 5765) covalent geometry : angle 0.64330 ( 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: 35 poor density : 74 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7758 (p0) cc_final: 0.6867 (p0) REVERT: A 78 GLN cc_start: 0.7185 (mp10) cc_final: 0.6890 (mp10) REVERT: B 26 GLN cc_start: 0.6608 (mt0) cc_final: 0.6294 (mm-40) REVERT: B 149 GLU cc_start: 0.7170 (tp30) cc_final: 0.6855 (mm-30) REVERT: B 253 ASP cc_start: 0.6818 (t70) cc_final: 0.6616 (t0) REVERT: B 257 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6678 (mm) REVERT: C 105 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.6895 (m-80) REVERT: C 110 TRP cc_start: 0.7101 (p-90) cc_final: 0.6816 (p-90) outliers start: 35 outliers final: 24 residues processed: 106 average time/residue: 0.1803 time to fit residues: 24.8349 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 : 0.668 ------------------------------------------------------------------------------- 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 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 184 VAL 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 Chi-restraints excluded: chain C residue 367 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.205396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.162995 restraints weight = 7454.613| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.33 r_work: 0.3693 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5776 Z= 0.164 Angle : 0.634 6.252 7875 Z= 0.314 Chirality : 0.043 0.151 871 Planarity : 0.005 0.060 1011 Dihedral : 5.747 55.578 766 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.98 % Allowed : 27.45 % Favored : 67.58 % 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: -1.16 (0.34), residues: 695 helix: 1.67 (0.51), residues: 117 sheet: -1.26 (0.41), residues: 169 loop : -1.30 (0.33), residues: 409 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 0.012 0.001 TYR C 69 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 137) hydrogen bonds : angle 5.79830 ( 357) SS BOND : bond 0.00437 ( 11) SS BOND : angle 1.62264 ( 22) covalent geometry : bond 0.00387 ( 5765) covalent geometry : angle 0.62921 ( 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 104 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7746 (p0) cc_final: 0.6838 (p0) REVERT: A 78 GLN cc_start: 0.7142 (mp10) cc_final: 0.6859 (mp10) REVERT: B 26 GLN cc_start: 0.6562 (mt0) cc_final: 0.6189 (mm-40) REVERT: B 149 GLU cc_start: 0.7140 (tp30) cc_final: 0.6831 (mm-30) REVERT: B 155 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: B 253 ASP cc_start: 0.6823 (t70) cc_final: 0.6602 (t0) REVERT: B 257 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6708 (mm) REVERT: C 105 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.6922 (m-80) outliers start: 31 outliers final: 26 residues processed: 102 average time/residue: 0.1893 time to fit residues: 25.1001 Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 127 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 257 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 184 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 268 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 Chi-restraints excluded: chain C residue 367 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.206307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164573 restraints weight = 7524.128| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 3.33 r_work: 0.3699 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5776 Z= 0.152 Angle : 0.643 7.330 7875 Z= 0.315 Chirality : 0.042 0.145 871 Planarity : 0.005 0.059 1011 Dihedral : 5.722 56.661 766 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.98 % Allowed : 27.77 % 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: -1.08 (0.34), residues: 695 helix: 2.12 (0.51), residues: 111 sheet: -1.26 (0.41), residues: 171 loop : -1.31 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 110 HIS 0.002 0.000 HIS B 167 PHE 0.024 0.002 PHE C 105 TYR 0.027 0.002 TYR C 171 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 137) hydrogen bonds : angle 5.71455 ( 357) SS BOND : bond 0.00512 ( 11) SS BOND : angle 1.57790 ( 22) covalent geometry : bond 0.00360 ( 5765) covalent geometry : angle 0.63842 ( 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 105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7774 (p0) cc_final: 0.6867 (p0) REVERT: A 78 GLN cc_start: 0.7174 (mp10) cc_final: 0.6824 (mp10) REVERT: B 26 GLN cc_start: 0.6614 (mt0) cc_final: 0.6235 (mm-40) REVERT: B 149 GLU cc_start: 0.7105 (tp30) cc_final: 0.6783 (mm-30) REVERT: B 253 ASP cc_start: 0.6822 (t70) cc_final: 0.6607 (t0) REVERT: B 257 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6711 (mm) REVERT: C 105 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.6897 (m-80) outliers start: 31 outliers final: 26 residues processed: 103 average time/residue: 0.1820 time to fit residues: 24.8429 Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 127 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 257 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 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 268 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: 7.9990 chunk 29 optimal weight: 0.0020 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4286 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.208920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165713 restraints weight = 7489.788| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.19 r_work: 0.3744 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5776 Z= 0.128 Angle : 0.631 8.972 7875 Z= 0.307 Chirality : 0.041 0.139 871 Planarity : 0.005 0.058 1011 Dihedral : 5.629 56.370 766 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.82 % Allowed : 28.09 % Favored : 67.09 % 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: -0.97 (0.34), residues: 695 helix: 2.33 (0.51), residues: 111 sheet: -1.23 (0.40), residues: 171 loop : -1.25 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.002 0.000 HIS B 167 PHE 0.021 0.001 PHE C 105 TYR 0.026 0.002 TYR C 171 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 137) hydrogen bonds : angle 5.54196 ( 357) SS BOND : bond 0.00394 ( 11) SS BOND : angle 1.58357 ( 22) covalent geometry : bond 0.00298 ( 5765) covalent geometry : angle 0.62675 ( 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 101 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7552 (p0) cc_final: 0.6653 (p0) REVERT: A 78 GLN cc_start: 0.7116 (mp10) cc_final: 0.6793 (mp10) REVERT: B 26 GLN cc_start: 0.6479 (mt0) cc_final: 0.6089 (mm-40) REVERT: B 149 GLU cc_start: 0.7102 (tp30) cc_final: 0.6718 (mm-30) REVERT: B 253 ASP cc_start: 0.6755 (t70) cc_final: 0.6550 (t0) REVERT: B 257 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6638 (mm) REVERT: C 105 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6884 (m-80) outliers start: 30 outliers final: 24 residues processed: 101 average time/residue: 0.1938 time to fit residues: 25.7991 Evaluate side-chains 96 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 127 VAL Chi-restraints excluded: chain B residue 184 VAL 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 145 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 279 ILE 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: 3.9990 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 50 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.207625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165777 restraints weight = 7558.527| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.43 r_work: 0.3725 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5776 Z= 0.135 Angle : 0.640 8.408 7875 Z= 0.311 Chirality : 0.042 0.143 871 Planarity : 0.005 0.057 1011 Dihedral : 5.603 56.905 766 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.65 % Allowed : 27.93 % 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: -0.96 (0.34), residues: 695 helix: 2.32 (0.51), residues: 111 sheet: -1.21 (0.41), residues: 171 loop : -1.24 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 110 HIS 0.001 0.000 HIS B 167 PHE 0.022 0.001 PHE C 105 TYR 0.025 0.002 TYR C 171 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 137) hydrogen bonds : angle 5.51596 ( 357) SS BOND : bond 0.00485 ( 11) SS BOND : angle 1.51627 ( 22) covalent geometry : bond 0.00317 ( 5765) covalent geometry : angle 0.63606 ( 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 99 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.584 Fit side-chains REVERT: A 66 ASP cc_start: 0.7569 (p0) cc_final: 0.6666 (p0) REVERT: A 78 GLN cc_start: 0.7187 (mp10) cc_final: 0.6832 (mp10) REVERT: B 26 GLN cc_start: 0.6493 (mt0) cc_final: 0.6074 (mm-40) REVERT: B 149 GLU cc_start: 0.7075 (tp30) cc_final: 0.6709 (mm-30) REVERT: B 155 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: B 257 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6607 (mm) REVERT: C 105 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6796 (m-80) outliers start: 29 outliers final: 24 residues processed: 99 average time/residue: 0.1738 time to fit residues: 22.6290 Evaluate side-chains 95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 93 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 257 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 127 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 352 VAL 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: 0.6980 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.207919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165436 restraints weight = 7531.428| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.44 r_work: 0.3713 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5776 Z= 0.138 Angle : 0.637 8.324 7875 Z= 0.311 Chirality : 0.042 0.140 871 Planarity : 0.005 0.057 1011 Dihedral : 5.647 57.742 766 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.65 % Allowed : 28.57 % Favored : 66.77 % 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: 2.32 (0.51), residues: 111 sheet: -1.21 (0.41), residues: 166 loop : -1.18 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 110 HIS 0.002 0.000 HIS B 167 PHE 0.022 0.002 PHE C 105 TYR 0.025 0.002 TYR C 171 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 137) hydrogen bonds : angle 5.48085 ( 357) SS BOND : bond 0.00478 ( 11) SS BOND : angle 1.50233 ( 22) covalent geometry : bond 0.00325 ( 5765) covalent geometry : angle 0.63274 ( 7853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3446.57 seconds wall clock time: 60 minutes 48.75 seconds (3648.75 seconds total)