Starting phenix.real_space_refine on Tue Aug 4 13:03:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lfc_63044/08_2026/9lfc_63044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lfc_63044/08_2026/9lfc_63044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lfc_63044/08_2026/9lfc_63044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lfc_63044/08_2026/9lfc_63044.map" model { file = "/net/cci-nas-00/data/ceres_data/9lfc_63044/08_2026/9lfc_63044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lfc_63044/08_2026/9lfc_63044.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.057 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 11 5.16 5 C 2071 2.51 5 N 538 2.21 5 O 513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3133 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2402 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 649 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 96} Chain breaks: 3 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Unusual residues: {'ACE': 1} Classifications: {'peptide': 9, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4J2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.01, per 1000 atoms: 0.32 Number of scatterers: 3133 At special positions: 0 Unit cell: (68.82, 60.45, 110.67, 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 11 16.00 O 513 8.00 N 538 7.00 C 2071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 118.4 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 B 9 " Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 62.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 29 through 64 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 70 through 89 removed outlier: 3.710A pdb=" N GLY A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 3.523A pdb=" N ASN A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 140 removed outlier: 4.176A pdb=" N LEU A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 174 Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 195 through 211 removed outlier: 4.106A pdb=" N LEU A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 231 Processing helix chain 'A' and resid 238 through 278 Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 283 through 315 removed outlier: 4.420A pdb=" N SER A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 327 removed outlier: 3.867A pdb=" N ARG A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.571A pdb=" N GLN A 179 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 188 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 9 Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.508A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU C 33 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARG C 102 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 35 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.508A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU C 33 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARG C 102 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 35 " --> pdb=" O GLU C 100 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.49 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 743 1.33 - 1.45: 734 1.45 - 1.57: 1726 1.57 - 1.69: 0 1.69 - 1.82: 13 Bond restraints: 3216 Sorted by residual: bond pdb=" N ILE A 190 " pdb=" CA ILE A 190 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.15e-02 7.56e+03 1.07e+01 bond pdb=" C ARG B 3 " pdb=" O ARG B 3 " ideal model delta sigma weight residual 1.241 1.211 0.029 1.33e-02 5.65e+03 4.88e+00 bond pdb=" N LEU A 192 " pdb=" CA LEU A 192 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.28e-02 6.10e+03 4.32e+00 bond pdb=" N LEU A 191 " pdb=" CA LEU A 191 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.28e-02 6.10e+03 4.13e+00 bond pdb=" N ALA C 76 " pdb=" CA ALA C 76 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.54e+00 ... (remaining 3211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 4226 1.47 - 2.93: 117 2.93 - 4.40: 30 4.40 - 5.87: 17 5.87 - 7.33: 3 Bond angle restraints: 4393 Sorted by residual: angle pdb=" N GLU A 273 " pdb=" CA GLU A 273 " pdb=" C GLU A 273 " ideal model delta sigma weight residual 110.97 106.74 4.23 1.09e+00 8.42e-01 1.51e+01 angle pdb=" CA ILE A 190 " pdb=" C ILE A 190 " pdb=" O ILE A 190 " ideal model delta sigma weight residual 121.75 117.63 4.12 1.18e+00 7.18e-01 1.22e+01 angle pdb=" CA LEU A 191 " pdb=" C LEU A 191 " pdb=" O LEU A 191 " ideal model delta sigma weight residual 121.58 117.96 3.62 1.12e+00 7.97e-01 1.04e+01 angle pdb=" C GLU A 273 " pdb=" N PHE A 274 " pdb=" CA PHE A 274 " ideal model delta sigma weight residual 120.38 116.06 4.32 1.37e+00 5.33e-01 9.96e+00 angle pdb=" N ASP C 74 " pdb=" CA ASP C 74 " pdb=" C ASP C 74 " ideal model delta sigma weight residual 109.72 114.50 -4.78 1.60e+00 3.91e-01 8.94e+00 ... (remaining 4388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.84: 1584 19.84 - 39.68: 202 39.68 - 59.51: 37 59.51 - 79.35: 6 79.35 - 99.19: 1 Dihedral angle restraints: 1830 sinusoidal: 652 harmonic: 1178 Sorted by residual: dihedral pdb=" CA SER B 8 " pdb=" C SER B 8 " pdb=" N 4J2 B 9 " pdb=" CA 4J2 B 9 " ideal model delta harmonic sigma weight residual 180.00 80.81 99.19 0 5.00e+00 4.00e-02 3.94e+02 dihedral pdb=" CA PHE B 7 " pdb=" C PHE B 7 " pdb=" N SER B 8 " pdb=" CA SER B 8 " ideal model delta harmonic sigma weight residual -180.00 -109.01 -70.99 0 5.00e+00 4.00e-02 2.02e+02 dihedral pdb=" CA 4J2 B 9 " pdb=" C 4J2 B 9 " pdb=" N ILE B 10 " pdb=" CA ILE B 10 " ideal model delta harmonic sigma weight residual -180.00 -114.78 -65.22 0 5.00e+00 4.00e-02 1.70e+02 ... (remaining 1827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 437 0.062 - 0.123: 64 0.123 - 0.185: 4 0.185 - 0.246: 1 0.246 - 0.308: 1 Chirality restraints: 507 Sorted by residual: chirality pdb=" CA ASP C 74 " pdb=" N ASP C 74 " pdb=" C ASP C 74 " pdb=" CB ASP C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA LEU A 192 " pdb=" N LEU A 192 " pdb=" C LEU A 192 " pdb=" CB LEU A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 504 not shown) Planarity restraints: 548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE B 1 " -0.025 2.00e-02 2.50e+03 8.27e-02 8.55e+01 pdb=" O ACE B 1 " -0.014 2.00e-02 2.50e+03 pdb=" CH3 ACE B 1 " 0.074 2.00e-02 2.50e+03 pdb=" N LYS B 2 " -0.134 2.00e-02 2.50e+03 pdb=" CA LYS B 2 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 3 " 0.489 9.50e-02 1.11e+02 2.19e-01 2.94e+01 pdb=" NE ARG B 3 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 3 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 3 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 3 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 189 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C CYS A 189 " 0.043 2.00e-02 2.50e+03 pdb=" O CYS A 189 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 190 " -0.014 2.00e-02 2.50e+03 ... (remaining 545 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 896 2.81 - 3.33: 3055 3.33 - 3.85: 5401 3.85 - 4.38: 5550 4.38 - 4.90: 10132 Nonbonded interactions: 25034 Sorted by model distance: nonbonded pdb=" N GLN A 148 " pdb=" OE1 GLN A 148 " model vdw 2.285 3.120 nonbonded pdb=" O TRP A 98 " pdb=" NE2 GLN A 100 " model vdw 2.333 3.120 nonbonded pdb=" O GLU A 95 " pdb=" ND2 ASN A 99 " model vdw 2.359 3.120 nonbonded pdb=" O THR A 187 " pdb=" OG1 THR A 187 " model vdw 2.369 3.040 nonbonded pdb=" O LEU A 76 " pdb=" OH TYR A 312 " model vdw 2.383 3.040 ... (remaining 25029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.640 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 0.069 3218 Z= 0.230 Angle : 0.701 7.334 4397 Z= 0.392 Chirality : 0.046 0.308 507 Planarity : 0.011 0.219 548 Dihedral : 17.315 99.191 1060 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.31 % Favored : 96.44 % Rotamer: Outliers : 1.33 % Allowed : 31.67 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.42), residues: 393 helix: 1.64 (0.31), residues: 245 sheet: 0.88 (0.76), residues: 55 loop : -2.42 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 3 TYR 0.015 0.002 TYR A 312 PHE 0.013 0.002 PHE B 7 TRP 0.012 0.001 TRP A 286 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 ( 3216) covalent geometry : angle 0.70015 / 0.39 ( 4393) SS BOND : bond 0.00263 / 0.13 ( 2) SS BOND : angle 1.08239 / 0.61 ( 4) hydrogen bonds : bond 0.11396 / 8.12 ( 233) hydrogen bonds : angle 5.29188 / 3.96 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.0453 time to fit residues: 3.8477 Evaluate side-chains 67 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 99 ASN A 224 HIS A 277 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.141223 restraints weight = 4455.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145464 restraints weight = 2347.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148156 restraints weight = 1648.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149448 restraints weight = 1335.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149663 restraints weight = 1195.455| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3218 Z= 0.179 Angle : 0.619 9.042 4397 Z= 0.316 Chirality : 0.044 0.321 507 Planarity : 0.004 0.034 548 Dihedral : 6.292 56.304 449 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.33 % Allowed : 27.67 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.41), residues: 393 helix: 1.74 (0.31), residues: 248 sheet: 0.91 (0.73), residues: 57 loop : -1.97 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.014 0.002 TYR A 312 PHE 0.009 0.001 PHE A 57 TRP 0.008 0.001 TRP A 286 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 3216) covalent geometry : angle 0.61900 / 0.32 ( 4393) SS BOND : bond 0.00327 / 0.16 ( 2) SS BOND : angle 0.92003 / 0.51 ( 4) hydrogen bonds : bond 0.04728 / 3.29 ( 233) hydrogen bonds : angle 4.47535 / 3.18 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TRP cc_start: 0.5859 (OUTLIER) cc_final: 0.5421 (m100) outliers start: 19 outliers final: 13 residues processed: 81 average time/residue: 0.0307 time to fit residues: 3.3379 Evaluate side-chains 76 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 98 TRP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain B residue 10 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.169624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143379 restraints weight = 4507.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147734 restraints weight = 2361.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150422 restraints weight = 1643.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.151798 restraints weight = 1324.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152359 restraints weight = 1181.979| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3218 Z= 0.148 Angle : 0.581 7.513 4397 Z= 0.292 Chirality : 0.043 0.304 507 Planarity : 0.004 0.032 548 Dihedral : 6.079 68.747 447 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 7.00 % Allowed : 27.33 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.41), residues: 393 helix: 1.91 (0.31), residues: 248 sheet: 0.89 (0.71), residues: 57 loop : -1.70 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.014 0.001 TYR A 312 PHE 0.013 0.001 PHE A 276 TRP 0.008 0.001 TRP A 286 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3216) covalent geometry : angle 0.58014 / 0.29 ( 4393) SS BOND : bond 0.00335 / 0.17 ( 2) SS BOND : angle 1.00078 / 0.56 ( 4) hydrogen bonds : bond 0.04274 / 2.95 ( 233) hydrogen bonds : angle 4.29646 / 3.02 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8553 (t70) cc_final: 0.8294 (t70) REVERT: A 98 TRP cc_start: 0.5841 (OUTLIER) cc_final: 0.5401 (m100) REVERT: A 196 GLU cc_start: 0.7403 (mp0) cc_final: 0.7195 (mt-10) REVERT: C 36 MET cc_start: 0.7939 (mtm) cc_final: 0.7681 (mtm) outliers start: 21 outliers final: 15 residues processed: 82 average time/residue: 0.0440 time to fit residues: 4.8168 Evaluate side-chains 79 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143020 restraints weight = 4436.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147359 restraints weight = 2355.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149894 restraints weight = 1648.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151266 restraints weight = 1341.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151274 restraints weight = 1195.954| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3218 Z= 0.148 Angle : 0.583 7.215 4397 Z= 0.290 Chirality : 0.042 0.285 507 Planarity : 0.003 0.032 548 Dihedral : 6.297 81.095 445 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 7.33 % Allowed : 27.67 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.41), residues: 393 helix: 1.96 (0.31), residues: 248 sheet: 0.97 (0.72), residues: 57 loop : -1.68 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.014 0.001 TYR A 312 PHE 0.014 0.001 PHE A 299 TRP 0.008 0.001 TRP A 286 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3216) covalent geometry : angle 0.58240 / 0.29 ( 4393) SS BOND : bond 0.00223 / 0.11 ( 2) SS BOND : angle 1.14573 / 0.63 ( 4) hydrogen bonds : bond 0.04187 / 2.88 ( 233) hydrogen bonds : angle 4.24566 / 2.97 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8607 (t70) cc_final: 0.8297 (t70) outliers start: 22 outliers final: 16 residues processed: 79 average time/residue: 0.0508 time to fit residues: 5.1688 Evaluate side-chains 77 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139693 restraints weight = 4456.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143995 restraints weight = 2340.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146648 restraints weight = 1630.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148198 restraints weight = 1316.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149045 restraints weight = 1165.431| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3218 Z= 0.168 Angle : 0.595 7.070 4397 Z= 0.299 Chirality : 0.043 0.302 507 Planarity : 0.004 0.033 548 Dihedral : 6.443 85.970 445 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 8.00 % Allowed : 27.00 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.41), residues: 393 helix: 1.90 (0.30), residues: 248 sheet: 0.98 (0.72), residues: 57 loop : -1.65 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.015 0.001 TYR A 312 PHE 0.013 0.001 PHE A 299 TRP 0.007 0.001 TRP A 286 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 3216) covalent geometry : angle 0.59437 / 0.30 ( 4393) SS BOND : bond 0.00444 / 0.22 ( 2) SS BOND : angle 1.15620 / 0.64 ( 4) hydrogen bonds : bond 0.04327 / 2.97 ( 233) hydrogen bonds : angle 4.27658 / 2.98 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TRP cc_start: 0.5852 (OUTLIER) cc_final: 0.5370 (m100) REVERT: A 189 CYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7282 (t) REVERT: A 196 GLU cc_start: 0.7416 (mp0) cc_final: 0.7143 (mt-10) outliers start: 24 outliers final: 19 residues processed: 81 average time/residue: 0.0348 time to fit residues: 3.7599 Evaluate side-chains 86 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 TRP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 35 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.169977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144447 restraints weight = 4413.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148725 restraints weight = 2280.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151444 restraints weight = 1584.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152825 restraints weight = 1269.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154017 restraints weight = 1125.768| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3218 Z= 0.128 Angle : 0.560 7.186 4397 Z= 0.279 Chirality : 0.041 0.253 507 Planarity : 0.003 0.033 548 Dihedral : 6.516 88.304 445 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 7.33 % Allowed : 27.33 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.41), residues: 393 helix: 2.06 (0.31), residues: 248 sheet: 1.09 (0.72), residues: 57 loop : -1.63 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 102 TYR 0.013 0.001 TYR A 312 PHE 0.011 0.001 PHE A 299 TRP 0.007 0.001 TRP A 286 HIS 0.006 0.002 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 3216) covalent geometry : angle 0.55921 / 0.28 ( 4393) SS BOND : bond 0.00227 / 0.11 ( 2) SS BOND : angle 1.02268 / 0.56 ( 4) hydrogen bonds : bond 0.04061 / 2.79 ( 233) hydrogen bonds : angle 4.18776 / 2.92 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 76 average time/residue: 0.0521 time to fit residues: 5.0839 Evaluate side-chains 77 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142536 restraints weight = 4475.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146906 restraints weight = 2346.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.149537 restraints weight = 1629.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.150945 restraints weight = 1321.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152119 restraints weight = 1173.271| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3218 Z= 0.150 Angle : 0.581 7.310 4397 Z= 0.291 Chirality : 0.042 0.268 507 Planarity : 0.004 0.033 548 Dihedral : 6.541 88.899 445 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 7.00 % Allowed : 28.33 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.41), residues: 393 helix: 2.02 (0.31), residues: 248 sheet: 1.11 (0.72), residues: 57 loop : -1.58 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 246 TYR 0.014 0.001 TYR A 312 PHE 0.009 0.001 PHE A 299 TRP 0.010 0.001 TRP A 286 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3216) covalent geometry : angle 0.58060 / 0.29 ( 4393) SS BOND : bond 0.00277 / 0.13 ( 2) SS BOND : angle 1.21710 / 0.67 ( 4) hydrogen bonds : bond 0.04168 / 2.86 ( 233) hydrogen bonds : angle 4.19429 / 2.93 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8690 (t70) cc_final: 0.8463 (t70) REVERT: A 98 TRP cc_start: 0.5851 (OUTLIER) cc_final: 0.5360 (m100) REVERT: A 189 CYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7177 (t) outliers start: 21 outliers final: 15 residues processed: 78 average time/residue: 0.0449 time to fit residues: 4.4776 Evaluate side-chains 83 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 TRP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143361 restraints weight = 4524.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147811 restraints weight = 2350.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150527 restraints weight = 1632.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152019 restraints weight = 1314.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152252 restraints weight = 1161.898| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3218 Z= 0.136 Angle : 0.572 7.301 4397 Z= 0.286 Chirality : 0.042 0.248 507 Planarity : 0.004 0.033 548 Dihedral : 6.552 89.240 445 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.67 % Allowed : 28.33 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.42), residues: 393 helix: 2.08 (0.31), residues: 248 sheet: 0.69 (0.68), residues: 63 loop : -1.50 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.013 0.001 TYR A 312 PHE 0.010 0.001 PHE A 299 TRP 0.010 0.001 TRP A 286 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3216) covalent geometry : angle 0.57117 / 0.29 ( 4393) SS BOND : bond 0.00234 / 0.11 ( 2) SS BOND : angle 1.10968 / 0.61 ( 4) hydrogen bonds : bond 0.04065 / 2.79 ( 233) hydrogen bonds : angle 4.16729 / 2.90 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8698 (t70) cc_final: 0.8436 (t70) REVERT: A 98 TRP cc_start: 0.5820 (OUTLIER) cc_final: 0.5257 (m100) REVERT: A 100 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7543 (mt0) REVERT: A 189 CYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7170 (t) outliers start: 20 outliers final: 16 residues processed: 75 average time/residue: 0.0454 time to fit residues: 4.5026 Evaluate side-chains 81 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 TRP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141967 restraints weight = 4505.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146328 restraints weight = 2367.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148659 restraints weight = 1650.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150504 restraints weight = 1358.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.151260 restraints weight = 1187.794| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3218 Z= 0.158 Angle : 0.590 7.361 4397 Z= 0.295 Chirality : 0.042 0.263 507 Planarity : 0.004 0.034 548 Dihedral : 6.553 88.814 445 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 8.00 % Allowed : 27.00 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.41), residues: 393 helix: 2.00 (0.31), residues: 248 sheet: 0.60 (0.69), residues: 63 loop : -1.51 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 246 TYR 0.015 0.001 TYR A 312 PHE 0.010 0.001 PHE A 57 TRP 0.011 0.001 TRP A 286 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 3216) covalent geometry : angle 0.58898 / 0.30 ( 4393) SS BOND : bond 0.00290 / 0.14 ( 2) SS BOND : angle 1.10851 / 0.61 ( 4) hydrogen bonds : bond 0.04193 / 2.88 ( 233) hydrogen bonds : angle 4.20516 / 2.93 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8730 (t70) cc_final: 0.8455 (t70) REVERT: A 98 TRP cc_start: 0.5847 (OUTLIER) cc_final: 0.5285 (m100) REVERT: A 100 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7574 (mt0) REVERT: A 189 CYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7238 (t) outliers start: 24 outliers final: 18 residues processed: 84 average time/residue: 0.0488 time to fit residues: 5.2907 Evaluate side-chains 83 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 TRP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.167935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142072 restraints weight = 4425.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146274 restraints weight = 2330.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148805 restraints weight = 1635.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150294 restraints weight = 1335.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.151212 restraints weight = 1182.912| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3218 Z= 0.163 Angle : 0.607 7.269 4397 Z= 0.306 Chirality : 0.043 0.265 507 Planarity : 0.004 0.034 548 Dihedral : 6.561 88.304 445 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 7.67 % Allowed : 27.67 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.41), residues: 393 helix: 2.00 (0.31), residues: 247 sheet: 1.54 (0.77), residues: 49 loop : -1.45 (0.59), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 246 TYR 0.016 0.001 TYR A 312 PHE 0.014 0.001 PHE A 276 TRP 0.010 0.001 TRP A 286 HIS 0.009 0.002 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 3216) covalent geometry : angle 0.60618 / 0.31 ( 4393) SS BOND : bond 0.00269 / 0.13 ( 2) SS BOND : angle 1.10949 / 0.61 ( 4) hydrogen bonds : bond 0.04192 / 2.87 ( 233) hydrogen bonds : angle 4.22586 / 2.95 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8750 (t70) cc_final: 0.8333 (t70) REVERT: A 98 TRP cc_start: 0.5935 (OUTLIER) cc_final: 0.5363 (m100) REVERT: A 100 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7523 (mt0) REVERT: A 189 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7210 (t) outliers start: 23 outliers final: 17 residues processed: 80 average time/residue: 0.0467 time to fit residues: 4.7938 Evaluate side-chains 79 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 TRP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.167292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140832 restraints weight = 4495.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145157 restraints weight = 2369.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147791 restraints weight = 1653.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149525 restraints weight = 1340.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150427 restraints weight = 1171.342| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3218 Z= 0.163 Angle : 0.611 7.210 4397 Z= 0.306 Chirality : 0.043 0.288 507 Planarity : 0.004 0.033 548 Dihedral : 6.600 88.762 445 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 7.00 % Allowed : 29.00 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.41), residues: 393 helix: 1.98 (0.31), residues: 247 sheet: 1.54 (0.78), residues: 49 loop : -1.52 (0.58), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 246 TYR 0.016 0.001 TYR A 312 PHE 0.013 0.001 PHE A 299 TRP 0.011 0.001 TRP A 286 HIS 0.008 0.002 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 3216) covalent geometry : angle 0.61026 / 0.31 ( 4393) SS BOND : bond 0.00286 / 0.14 ( 2) SS BOND : angle 1.10764 / 0.61 ( 4) hydrogen bonds : bond 0.04216 / 2.88 ( 233) hydrogen bonds : angle 4.23862 / 2.95 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 737.54 seconds wall clock time: 13 minutes 20.10 seconds (800.10 seconds total)