Starting phenix.real_space_refine on Thu Mar 6 09:01:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vu5_43526/03_2025/8vu5_43526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vu5_43526/03_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_43526/03_2025/8vu5_43526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vu5_43526/03_2025/8vu5_43526.map" model { file = "/net/cci-nas-00/data/ceres_data/8vu5_43526/03_2025/8vu5_43526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vu5_43526/03_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-5624/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: 4.06, per 1000 atoms: 0.72 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: 1.26 Conformation dependent library (CDL) restraints added in 628.5 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: 0.65 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: 1.22 Time building geometry restraints manager: 1.52 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: 1.990 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.790 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- 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 5765 Z= 0.341 Angle : 0.807 9.994 7853 Z= 0.478 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 *********************** 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 : 0.597 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: 0.1644 time to fit residues: 18.6669 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 : 0.598 ------------------------------------------------------------------------------- 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 5765 Z= 0.178 Angle : 0.636 8.467 7853 Z= 0.320 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 *********************** 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 : 0.749 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: 0.1813 time to fit residues: 24.4167 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 : 0.635 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 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 5765 Z= 0.265 Angle : 0.629 6.503 7853 Z= 0.316 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 *********************** 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 : 0.638 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: 0.2068 time to fit residues: 28.8650 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 : 0.629 ------------------------------------------------------------------------------- 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 5765 Z= 0.189 Angle : 0.620 7.620 7853 Z= 0.306 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 *********************** 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 : 0.605 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: 0.1792 time to fit residues: 23.4804 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 : 0.668 ------------------------------------------------------------------------------- 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 5765 Z= 0.255 Angle : 0.635 6.501 7853 Z= 0.315 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 *********************** 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 : 0.685 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: 0.1884 time to fit residues: 25.5447 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 : 0.641 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.9990 chunk 3 optimal weight: 0.0770 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 = 0.206044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.163777 restraints weight = 7394.696| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.40 r_work: 0.3692 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5765 Z= 0.248 Angle : 0.624 8.663 7853 Z= 0.307 Chirality : 0.042 0.145 871 Planarity : 0.005 0.059 1011 Dihedral : 5.680 55.361 766 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.14 % Allowed : 27.29 % 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: 1.73 (0.51), residues: 117 sheet: -1.27 (0.40), residues: 176 loop : -1.32 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 198 HIS 0.002 0.000 HIS C 367 PHE 0.025 0.002 PHE C 105 TYR 0.020 0.002 TYR C 80 ARG 0.003 0.000 ARG C 249 *********************** 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 105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7647 (p0) cc_final: 0.6765 (p0) REVERT: A 78 GLN cc_start: 0.7165 (mp10) cc_final: 0.6876 (mp10) REVERT: B 26 GLN cc_start: 0.6537 (mt0) cc_final: 0.6248 (mm-40) REVERT: B 149 GLU cc_start: 0.7099 (tp30) cc_final: 0.6772 (mm-30) REVERT: B 257 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6600 (mm) REVERT: C 105 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: C 110 TRP cc_start: 0.7056 (p-90) cc_final: 0.6799 (p-90) outliers start: 32 outliers final: 25 residues processed: 102 average time/residue: 0.1939 time to fit residues: 25.5719 Evaluate side-chains 96 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.0020 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.4488 r_free = 0.4488 target = 0.207489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165487 restraints weight = 7459.175| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.36 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: 0.7166 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5765 Z= 0.215 Angle : 0.611 6.070 7853 Z= 0.301 Chirality : 0.042 0.151 871 Planarity : 0.005 0.058 1011 Dihedral : 5.623 55.638 766 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.33 % Allowed : 27.77 % 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: -1.06 (0.34), residues: 695 helix: 1.91 (0.51), residues: 117 sheet: -1.24 (0.40), residues: 176 loop : -1.26 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.002 0.000 HIS B 153 PHE 0.023 0.002 PHE C 105 TYR 0.010 0.001 TYR C 69 ARG 0.003 0.000 ARG C 249 *********************** 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: 27 poor density : 76 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7642 (p0) cc_final: 0.6758 (p0) REVERT: A 78 GLN cc_start: 0.7166 (mp10) cc_final: 0.6891 (mp10) REVERT: B 26 GLN cc_start: 0.6448 (mt0) cc_final: 0.6093 (mm-40) REVERT: B 149 GLU cc_start: 0.7126 (tp30) cc_final: 0.6784 (mm-30) REVERT: B 257 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6626 (mm) REVERT: C 105 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: C 110 TRP cc_start: 0.6996 (p-90) cc_final: 0.6754 (p-90) outliers start: 27 outliers final: 22 residues processed: 102 average time/residue: 0.1849 time to fit residues: 24.4458 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 : 0.598 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.207858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.166085 restraints weight = 7457.487| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 3.35 r_work: 0.3735 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5765 Z= 0.201 Angle : 0.616 7.699 7853 Z= 0.301 Chirality : 0.042 0.146 871 Planarity : 0.005 0.057 1011 Dihedral : 5.584 56.495 766 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.49 % Allowed : 27.61 % 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: -1.03 (0.34), residues: 695 helix: 1.93 (0.51), residues: 117 sheet: -1.18 (0.41), residues: 171 loop : -1.26 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 52 HIS 0.001 0.000 HIS B 167 PHE 0.022 0.002 PHE C 105 TYR 0.020 0.001 TYR C 80 ARG 0.003 0.000 ARG C 166 *********************** 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 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7604 (p0) cc_final: 0.6719 (p0) REVERT: A 78 GLN cc_start: 0.7178 (mp10) cc_final: 0.6871 (mp10) REVERT: B 26 GLN cc_start: 0.6417 (mt0) cc_final: 0.6087 (mm-40) REVERT: B 149 GLU cc_start: 0.7035 (tp30) cc_final: 0.6668 (mm-30) REVERT: B 155 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: B 257 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6600 (mm) REVERT: C 105 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6899 (m-80) outliers start: 28 outliers final: 23 residues processed: 97 average time/residue: 0.1856 time to fit residues: 23.3883 Evaluate side-chains 93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 355 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 0.0050 chunk 46 optimal weight: 0.0980 chunk 41 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.210164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.167176 restraints weight = 7487.288| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.17 r_work: 0.3771 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5765 Z= 0.180 Angle : 0.616 9.025 7853 Z= 0.300 Chirality : 0.041 0.140 871 Planarity : 0.005 0.056 1011 Dihedral : 5.531 56.255 766 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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: -0.92 (0.34), residues: 695 helix: 2.05 (0.51), residues: 117 sheet: -1.15 (0.41), residues: 171 loop : -1.19 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 110 HIS 0.001 0.000 HIS B 167 PHE 0.020 0.001 PHE C 105 TYR 0.009 0.001 TYR C 67 ARG 0.005 0.000 ARG C 102 *********************** 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 97 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.665 Fit side-chains REVERT: A 66 ASP cc_start: 0.7460 (p0) cc_final: 0.6586 (p0) REVERT: A 78 GLN cc_start: 0.7103 (mp10) cc_final: 0.6843 (mp10) REVERT: B 26 GLN cc_start: 0.6374 (mt0) cc_final: 0.6074 (mm-40) REVERT: B 149 GLU cc_start: 0.6968 (tp30) cc_final: 0.6601 (mm-30) REVERT: B 257 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6572 (mm) REVERT: C 105 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6766 (m-80) outliers start: 26 outliers final: 22 residues processed: 97 average time/residue: 0.1978 time to fit residues: 24.9426 Evaluate side-chains 92 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 268 VAL 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 30 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.208105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164491 restraints weight = 7537.580| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.24 r_work: 0.3722 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5765 Z= 0.234 Angle : 0.633 7.521 7853 Z= 0.312 Chirality : 0.042 0.143 871 Planarity : 0.005 0.057 1011 Dihedral : 5.589 56.055 766 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % 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: -0.91 (0.34), residues: 695 helix: 2.26 (0.51), residues: 111 sheet: -1.18 (0.41), residues: 171 loop : -1.17 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 198 HIS 0.002 0.000 HIS B 167 PHE 0.023 0.002 PHE C 105 TYR 0.020 0.002 TYR C 80 ARG 0.004 0.000 ARG C 102 ********************** 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 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7605 (p0) cc_final: 0.6756 (p0) REVERT: A 78 GLN cc_start: 0.7138 (mp10) cc_final: 0.6863 (mp10) REVERT: B 26 GLN cc_start: 0.6404 (mt0) cc_final: 0.6122 (mm-40) REVERT: B 149 GLU cc_start: 0.7090 (tp30) cc_final: 0.6732 (mm-30) REVERT: B 155 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: B 257 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6526 (mm) REVERT: C 105 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6823 (m-80) outliers start: 31 outliers final: 23 residues processed: 100 average time/residue: 0.1857 time to fit residues: 24.1132 Evaluate side-chains 94 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 93 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.1980 chunk 63 optimal weight: 0.0060 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.209891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166424 restraints weight = 7539.367| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 3.26 r_work: 0.3750 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5765 Z= 0.189 Angle : 0.625 7.586 7853 Z= 0.304 Chirality : 0.042 0.143 871 Planarity : 0.005 0.056 1011 Dihedral : 5.568 56.695 766 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.82 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: -0.86 (0.34), residues: 695 helix: 2.37 (0.51), residues: 111 sheet: -1.18 (0.41), residues: 171 loop : -1.15 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.001 0.000 HIS B 167 PHE 0.021 0.001 PHE C 105 TYR 0.007 0.001 TYR C 69 ARG 0.004 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3255.29 seconds wall clock time: 56 minutes 30.47 seconds (3390.47 seconds total)