Starting phenix.real_space_refine on Thu Oct 22 20:51:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbu_52030/10_2026/9hbu_52030.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbu_52030/10_2026/9hbu_52030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hbu_52030/10_2026/9hbu_52030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbu_52030/10_2026/9hbu_52030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hbu_52030/10_2026/9hbu_52030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbu_52030/10_2026/9hbu_52030.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 34 5.16 5 C 3376 2.51 5 N 980 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5530 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2244 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 147 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 717 Classifications: {'RNA': 37} Modifications used: {'rna2p': 5, 'rna3p': 32} Link IDs: {'rna2p': 5, 'rna3p': 31} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Time building chain proxies: 1.24, per 1000 atoms: 0.22 Number of scatterers: 5530 At special positions: 0 Unit cell: (100.284, 82.2, 87.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 37 15.00 O 1103 8.00 N 980 7.00 C 3376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.40 Conformation dependent library (CDL) restraints added in 158.2 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 52.8% alpha, 4.6% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 36 through 51 removed outlier: 4.081A pdb=" N PHE C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 118 through 127 removed outlier: 4.540A pdb=" N GLU C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 173 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.640A pdb=" N LEU C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 340 through 350 Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 58 through 74 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.577A pdb=" N TYR D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 143 through 173 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.966A pdb=" N LEU D 266 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 340 through 350 Processing sheet with id=AA1, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'C' and resid 247 through 248 Processing sheet with id=AA3, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AA4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'D' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'D' and resid 284 through 286 229 hydrogen bonds defined for protein. 651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1691 1.34 - 1.46: 1418 1.46 - 1.58: 2474 1.58 - 1.69: 72 1.69 - 1.81: 46 Bond restraints: 5701 Sorted by residual: bond pdb=" N3 Y5P H 14 " pdb=" C4 Y5P H 14 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" N3 Y5P H 19 " pdb=" C4 Y5P H 19 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" N3 Y5P H 26 " pdb=" C4 Y5P H 26 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" N3 Y5P H 12 " pdb=" C4 Y5P H 12 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" N3 Y5P H 20 " pdb=" C4 Y5P H 20 " ideal model delta sigma weight residual 1.458 1.334 0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 5696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 7523 2.39 - 4.77: 189 4.77 - 7.16: 57 7.16 - 9.54: 30 9.54 - 11.93: 14 Bond angle restraints: 7813 Sorted by residual: angle pdb=" N1 Y5P H 8 " pdb=" C2 Y5P H 8 " pdb=" N3 Y5P H 8 " ideal model delta sigma weight residual 126.68 114.75 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N1 Y5P H 6 " pdb=" C2 Y5P H 6 " pdb=" N3 Y5P H 6 " ideal model delta sigma weight residual 126.68 114.83 11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N1 Y5P H 7 " pdb=" C2 Y5P H 7 " pdb=" N3 Y5P H 7 " ideal model delta sigma weight residual 126.68 114.83 11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N1 Y5P H 39 " pdb=" C2 Y5P H 39 " pdb=" N3 Y5P H 39 " ideal model delta sigma weight residual 126.68 114.85 11.83 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N1 Y5P H 5 " pdb=" C2 Y5P H 5 " pdb=" N3 Y5P H 5 " ideal model delta sigma weight residual 126.68 114.85 11.83 3.00e+00 1.11e-01 1.55e+01 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 3823 35.52 - 71.04: 188 71.04 - 106.56: 88 106.56 - 142.09: 1 142.09 - 177.61: 2 Dihedral angle restraints: 4102 sinusoidal: 2313 harmonic: 1789 Sorted by residual: dihedral pdb=" P Y5P H 6 " pdb=" O5' Y5P H 6 " pdb=" C5' Y5P H 6 " pdb=" C4' Y5P H 6 " ideal model delta sinusoidal sigma weight residual 248.90 71.29 177.61 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" P Y5P H 37 " pdb=" O5' Y5P H 37 " pdb=" C5' Y5P H 37 " pdb=" C4' Y5P H 37 " ideal model delta sinusoidal sigma weight residual -111.10 59.04 -170.14 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" P Y5P H 19 " pdb=" O5' Y5P H 19 " pdb=" C5' Y5P H 19 " pdb=" C4' Y5P H 19 " ideal model delta sinusoidal sigma weight residual 248.90 140.01 108.89 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 4099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 572 0.026 - 0.051: 220 0.051 - 0.077: 44 0.077 - 0.103: 25 0.103 - 0.128: 22 Chirality restraints: 883 Sorted by residual: chirality pdb=" CA ILE C 230 " pdb=" N ILE C 230 " pdb=" C ILE C 230 " pdb=" CB ILE C 230 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE D 325 " pdb=" N ILE D 325 " pdb=" C ILE D 325 " pdb=" CB ILE D 325 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE D 305 " pdb=" N ILE D 305 " pdb=" C ILE D 305 " pdb=" CB ILE D 305 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 880 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' P5P H 35 " 0.015 2.00e-02 2.50e+03 7.91e-03 1.57e+00 pdb=" N9 P5P H 35 " -0.019 2.00e-02 2.50e+03 pdb=" C8 P5P H 35 " -0.000 2.00e-02 2.50e+03 pdb=" N7 P5P H 35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 P5P H 35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 P5P H 35 " 0.004 2.00e-02 2.50e+03 pdb=" N1 P5P H 35 " 0.003 2.00e-02 2.50e+03 pdb=" C2 P5P H 35 " -0.001 2.00e-02 2.50e+03 pdb=" N3 P5P H 35 " -0.003 2.00e-02 2.50e+03 pdb=" C4 P5P H 35 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' P5P H 34 " 0.012 2.00e-02 2.50e+03 6.72e-03 1.13e+00 pdb=" N9 P5P H 34 " -0.017 2.00e-02 2.50e+03 pdb=" C8 P5P H 34 " -0.002 2.00e-02 2.50e+03 pdb=" N7 P5P H 34 " 0.003 2.00e-02 2.50e+03 pdb=" C5 P5P H 34 " 0.001 2.00e-02 2.50e+03 pdb=" C6 P5P H 34 " 0.002 2.00e-02 2.50e+03 pdb=" N1 P5P H 34 " 0.001 2.00e-02 2.50e+03 pdb=" C2 P5P H 34 " -0.002 2.00e-02 2.50e+03 pdb=" N3 P5P H 34 " -0.001 2.00e-02 2.50e+03 pdb=" C4 P5P H 34 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' P5P H 4 " 0.012 2.00e-02 2.50e+03 6.11e-03 9.34e-01 pdb=" N9 P5P H 4 " -0.014 2.00e-02 2.50e+03 pdb=" C8 P5P H 4 " -0.000 2.00e-02 2.50e+03 pdb=" N7 P5P H 4 " 0.002 2.00e-02 2.50e+03 pdb=" C5 P5P H 4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 P5P H 4 " 0.002 2.00e-02 2.50e+03 pdb=" N1 P5P H 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 P5P H 4 " -0.000 2.00e-02 2.50e+03 pdb=" N3 P5P H 4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 P5P H 4 " -0.003 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 565 2.74 - 3.28: 5324 3.28 - 3.82: 9050 3.82 - 4.36: 10335 4.36 - 4.90: 17561 Nonbonded interactions: 42835 Sorted by model distance: nonbonded pdb=" O SER C 113 " pdb=" OG SER C 113 " model vdw 2.202 3.040 nonbonded pdb=" O SER D 113 " pdb=" OG SER D 113 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG C 112 " pdb=" OP1 Y5P H 20 " model vdw 2.271 3.120 nonbonded pdb=" O GLY C 275 " pdb=" N GLY C 277 " model vdw 2.273 3.120 nonbonded pdb=" O PHE D 294 " pdb=" OG SER D 308 " model vdw 2.334 3.040 ... (remaining 42830 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 'C' selection = (chain 'D' and (resid 34 through 290 or resid 317 through 350)) } 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: 0.010 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.560 Find NCS groups from input model: 0.070 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.012 0.125 5701 Z= 0.586 Angle : 1.109 11.929 7813 Z= 0.410 Chirality : 0.034 0.128 883 Planarity : 0.002 0.023 883 Dihedral : 22.703 177.607 2952 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 2.17 % Allowed : 18.90 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.27 (0.36), residues: 621 helix: 1.74 (0.32), residues: 309 sheet: -0.44 (1.07), residues: 24 loop : 0.05 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 92 TYR 0.004 0.001 TYR D 197 PHE 0.006 0.001 PHE D 208 TRP 0.008 0.001 TRP D 259 HIS 0.005 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.01177 / 0.59 ( 5701) covalent geometry : angle 1.10866 / 0.41 ( 7813) hydrogen bonds : bond 0.16476 / 11.60 ( 229) hydrogen bonds : angle 4.91415 / 3.53 ( 651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 279 ILE cc_start: 0.6174 (OUTLIER) cc_final: 0.5892 (mp) REVERT: D 49 VAL cc_start: 0.8420 (t) cc_final: 0.8142 (t) REVERT: D 146 MET cc_start: 0.6990 (tpt) cc_final: 0.5677 (tpt) REVERT: D 226 GLN cc_start: 0.7530 (tt0) cc_final: 0.7182 (tt0) REVERT: D 303 SER cc_start: 0.8473 (t) cc_final: 0.7692 (p) outliers start: 11 outliers final: 4 residues processed: 95 average time/residue: 0.1069 time to fit residues: 12.3284 Evaluate side-chains 72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [49, 53, 5, 33, 62, 51, 38, 61, 45, 27, 64] chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 326 GLN ** 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 = 0.4497 r_free = 0.4497 target = 0.230600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180556 restraints weight = 6398.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.180545 restraints weight = 5545.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.183001 restraints weight = 5141.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.183123 restraints weight = 4250.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.183410 restraints weight = 3924.528| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5701 Z= 0.153 Angle : 0.633 5.785 7813 Z= 0.299 Chirality : 0.037 0.151 883 Planarity : 0.004 0.054 883 Dihedral : 23.593 177.247 1819 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.06 % Favored : 96.78 % Rotamer: Outliers : 1.77 % Allowed : 20.47 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.03 (0.35), residues: 621 helix: 1.42 (0.31), residues: 322 sheet: -0.41 (1.07), residues: 24 loop : 0.01 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 198 TYR 0.020 0.002 TYR C 207 PHE 0.008 0.001 PHE C 235 TRP 0.011 0.001 TRP D 259 HIS 0.006 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 5701) covalent geometry : angle 0.63292 / 0.30 ( 7813) hydrogen bonds : bond 0.04562 / 3.06 ( 229) hydrogen bonds : angle 4.11617 / 2.92 ( 651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6969 (mpt180) REVERT: C 119 ARG cc_start: 0.6182 (mmm160) cc_final: 0.5842 (mmm160) REVERT: C 279 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.6125 (mp) REVERT: D 49 VAL cc_start: 0.8286 (t) cc_final: 0.8021 (t) REVERT: D 146 MET cc_start: 0.6916 (tpt) cc_final: 0.6345 (tpp) REVERT: D 303 SER cc_start: 0.8369 (t) cc_final: 0.7792 (p) REVERT: D 341 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8390 (tt) outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.1065 time to fit residues: 9.5637 Evaluate side-chains 66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [21, 6, 11, 47, 28, 63, 32, 39, 40, 64, 31] chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN C 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.227286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.177975 restraints weight = 6343.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.178296 restraints weight = 5395.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.180174 restraints weight = 4879.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.180347 restraints weight = 4112.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180740 restraints weight = 3941.906| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5701 Z= 0.137 Angle : 0.607 7.282 7813 Z= 0.285 Chirality : 0.037 0.128 883 Planarity : 0.003 0.025 883 Dihedral : 23.482 175.508 1812 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.58 % Rotamer: Outliers : 1.77 % Allowed : 21.06 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.35), residues: 621 helix: 1.31 (0.31), residues: 322 sheet: -0.51 (1.06), residues: 24 loop : 0.01 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.021 0.002 TYR C 207 PHE 0.009 0.001 PHE C 208 TRP 0.010 0.001 TRP D 259 HIS 0.005 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 5701) covalent geometry : angle 0.60670 / 0.29 ( 7813) hydrogen bonds : bond 0.03932 / 2.65 ( 229) hydrogen bonds : angle 4.08694 / 2.89 ( 651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: C 112 ARG cc_start: 0.7251 (mmt180) cc_final: 0.7002 (mpt180) REVERT: C 119 ARG cc_start: 0.6301 (mmm160) cc_final: 0.5874 (mmm160) REVERT: C 279 ILE cc_start: 0.6351 (OUTLIER) cc_final: 0.6105 (mp) REVERT: D 146 MET cc_start: 0.6788 (tpt) cc_final: 0.6184 (tpp) REVERT: D 303 SER cc_start: 0.8283 (t) cc_final: 0.7739 (p) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.0960 time to fit residues: 8.1877 Evaluate side-chains 67 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 322 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [53, 5, 24, 9, 63, 22, 29, 58, 59, 1, 50] chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 326 GLN ** 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 = 0.4492 r_free = 0.4492 target = 0.231442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.181302 restraints weight = 6323.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.183585 restraints weight = 5269.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.185633 restraints weight = 4638.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.185750 restraints weight = 3834.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.185908 restraints weight = 3537.862| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5701 Z= 0.106 Angle : 0.589 6.340 7813 Z= 0.275 Chirality : 0.036 0.129 883 Planarity : 0.003 0.028 883 Dihedral : 23.307 174.742 1811 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 1.57 % Allowed : 22.05 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.02 (0.35), residues: 621 helix: 1.36 (0.31), residues: 324 sheet: -0.46 (1.05), residues: 24 loop : 0.07 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 251 TYR 0.021 0.002 TYR C 207 PHE 0.009 0.001 PHE C 208 TRP 0.009 0.001 TRP D 259 HIS 0.005 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 5701) covalent geometry : angle 0.58852 / 0.27 ( 7813) hydrogen bonds : bond 0.03459 / 2.32 ( 229) hydrogen bonds : angle 3.93349 / 2.79 ( 651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: C 112 ARG cc_start: 0.7187 (mmt180) cc_final: 0.6949 (mpt180) REVERT: C 119 ARG cc_start: 0.6270 (mmm160) cc_final: 0.5908 (mmm160) REVERT: C 238 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7739 (mt) REVERT: C 279 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.5952 (mm) REVERT: D 146 MET cc_start: 0.6798 (tpt) cc_final: 0.5710 (tpt) REVERT: D 303 SER cc_start: 0.8293 (t) cc_final: 0.7794 (p) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.0993 time to fit residues: 8.5421 Evaluate side-chains 66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 322 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [47, 32, 49, 0, 26, 6, 60, 43, 39, 44, 19] chunk 47 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 326 GLN ** 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 = 0.4480 r_free = 0.4480 target = 0.229928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.179235 restraints weight = 6438.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.181135 restraints weight = 5430.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183777 restraints weight = 4849.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.183760 restraints weight = 3721.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183943 restraints weight = 3666.401| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5701 Z= 0.129 Angle : 0.594 6.512 7813 Z= 0.277 Chirality : 0.036 0.132 883 Planarity : 0.003 0.031 883 Dihedral : 23.267 174.664 1811 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.09 % Favored : 97.75 % Rotamer: Outliers : 2.76 % Allowed : 21.85 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.35), residues: 621 helix: 1.28 (0.31), residues: 324 sheet: -0.51 (1.04), residues: 24 loop : 0.01 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.025 0.002 TYR D 197 PHE 0.009 0.001 PHE C 208 TRP 0.011 0.001 TRP D 259 HIS 0.005 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 5701) covalent geometry : angle 0.59358 / 0.28 ( 7813) hydrogen bonds : bond 0.03635 / 2.45 ( 229) hydrogen bonds : angle 3.99487 / 2.84 ( 651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: C 112 ARG cc_start: 0.7219 (mmt180) cc_final: 0.7004 (mpt180) REVERT: C 238 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7680 (mt) REVERT: C 279 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.5988 (mm) REVERT: D 146 MET cc_start: 0.6835 (tpt) cc_final: 0.6197 (tpp) REVERT: D 268 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: D 303 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7875 (p) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.0999 time to fit residues: 9.1194 Evaluate side-chains 74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [25, 43, 18, 32, 9, 27, 5, 52, 53, 4, 51] chunk 25 optimal weight: 0.0870 chunk 43 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.233638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.184501 restraints weight = 6395.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.187147 restraints weight = 5328.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.188946 restraints weight = 4674.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.189433 restraints weight = 3711.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.189833 restraints weight = 3500.696| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5701 Z= 0.084 Angle : 0.564 4.777 7813 Z= 0.261 Chirality : 0.035 0.125 883 Planarity : 0.003 0.025 883 Dihedral : 23.181 174.188 1811 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 2.17 % Allowed : 22.44 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.07 (0.35), residues: 621 helix: 1.39 (0.31), residues: 326 sheet: -0.44 (1.06), residues: 24 loop : 0.10 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 119 TYR 0.024 0.002 TYR D 197 PHE 0.011 0.001 PHE C 208 TRP 0.008 0.001 TRP D 259 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 ( 5701) covalent geometry : angle 0.56411 / 0.26 ( 7813) hydrogen bonds : bond 0.03103 / 2.06 ( 229) hydrogen bonds : angle 3.82583 / 2.74 ( 651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 LEU cc_start: 0.7952 (mp) cc_final: 0.7735 (mt) REVERT: C 112 ARG cc_start: 0.7066 (mmt180) cc_final: 0.6800 (mpt180) REVERT: C 238 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7694 (mt) REVERT: C 279 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.6075 (mm) REVERT: D 146 MET cc_start: 0.6825 (tpt) cc_final: 0.6157 (tpp) REVERT: D 268 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: D 303 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7786 (p) outliers start: 11 outliers final: 4 residues processed: 73 average time/residue: 0.0912 time to fit residues: 8.4526 Evaluate side-chains 71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 303 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [27, 6, 61, 44, 49, 32, 40, 10, 53, 28, 16] chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 326 GLN ** 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 = 0.4492 r_free = 0.4492 target = 0.230817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180246 restraints weight = 6427.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.180944 restraints weight = 5682.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.182883 restraints weight = 5125.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183321 restraints weight = 4080.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.183383 restraints weight = 3854.800| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5701 Z= 0.132 Angle : 0.597 6.525 7813 Z= 0.280 Chirality : 0.036 0.127 883 Planarity : 0.003 0.025 883 Dihedral : 23.191 173.998 1811 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.17 % Allowed : 22.83 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.35), residues: 621 helix: 1.30 (0.30), residues: 323 sheet: -0.54 (1.04), residues: 24 loop : 0.06 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 198 TYR 0.023 0.002 TYR D 197 PHE 0.012 0.001 PHE C 208 TRP 0.012 0.001 TRP D 259 HIS 0.005 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 5701) covalent geometry : angle 0.59723 / 0.28 ( 7813) hydrogen bonds : bond 0.03451 / 2.34 ( 229) hydrogen bonds : angle 3.91512 / 2.82 ( 651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 LEU cc_start: 0.7967 (mp) cc_final: 0.7719 (mt) REVERT: C 112 ARG cc_start: 0.7066 (mmt180) cc_final: 0.6803 (mpt180) REVERT: C 238 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7658 (mt) REVERT: D 146 MET cc_start: 0.6785 (tpt) cc_final: 0.6017 (tpp) REVERT: D 268 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6990 (mp0) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.0833 time to fit residues: 7.2054 Evaluate side-chains 70 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 268 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [9, 35, 54, 50, 32, 6, 52, 40, 39, 57, 56] chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.231458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182217 restraints weight = 6434.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.184276 restraints weight = 5647.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.185835 restraints weight = 4841.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.186026 restraints weight = 3759.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.186064 restraints weight = 3568.540| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5701 Z= 0.115 Angle : 0.584 5.632 7813 Z= 0.273 Chirality : 0.036 0.150 883 Planarity : 0.003 0.024 883 Dihedral : 23.164 173.719 1809 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.97 % Allowed : 23.82 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.35), residues: 621 helix: 1.24 (0.30), residues: 326 sheet: -0.52 (1.05), residues: 24 loop : 0.15 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 198 TYR 0.023 0.002 TYR D 197 PHE 0.012 0.001 PHE C 208 TRP 0.010 0.001 TRP D 259 HIS 0.004 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 5701) covalent geometry : angle 0.58367 / 0.27 ( 7813) hydrogen bonds : bond 0.03353 / 2.25 ( 229) hydrogen bonds : angle 3.90062 / 2.81 ( 651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 LEU cc_start: 0.7950 (mp) cc_final: 0.7710 (mt) REVERT: C 238 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7674 (mt) REVERT: D 146 MET cc_start: 0.6833 (tpt) cc_final: 0.6179 (tpp) REVERT: D 268 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6983 (mp0) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.0816 time to fit residues: 7.0014 Evaluate side-chains 67 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 268 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [18, 7, 1, 34, 45, 8, 3, 58, 54, 39, 38] chunk 18 optimal weight: 0.0000 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.232390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.182906 restraints weight = 6412.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183321 restraints weight = 5459.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.184989 restraints weight = 4876.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.185560 restraints weight = 4333.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.185829 restraints weight = 3900.646| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5701 Z= 0.101 Angle : 0.575 5.300 7813 Z= 0.268 Chirality : 0.035 0.128 883 Planarity : 0.003 0.024 883 Dihedral : 23.106 173.332 1809 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.17 % Allowed : 23.62 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.04 (0.35), residues: 621 helix: 1.30 (0.30), residues: 326 sheet: -0.48 (1.05), residues: 24 loop : 0.18 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 112 TYR 0.021 0.002 TYR D 197 PHE 0.012 0.001 PHE C 208 TRP 0.011 0.001 TRP C 259 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 5701) covalent geometry : angle 0.57539 / 0.27 ( 7813) hydrogen bonds : bond 0.03259 / 2.18 ( 229) hydrogen bonds : angle 3.89088 / 2.79 ( 651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 LEU cc_start: 0.7973 (mp) cc_final: 0.7736 (mt) REVERT: C 238 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7698 (mt) REVERT: D 146 MET cc_start: 0.6785 (tpt) cc_final: 0.6209 (tpp) REVERT: D 268 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6990 (mp0) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.0763 time to fit residues: 6.5481 Evaluate side-chains 66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 268 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [29, 40, 18, 45, 41, 38, 48, 64, 31, 7, 37] chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 0.0050 chunk 64 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 326 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 = 0.232156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.185435 restraints weight = 6452.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.186300 restraints weight = 5974.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.187465 restraints weight = 5075.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.187745 restraints weight = 4883.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.188936 restraints weight = 4133.562| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5701 Z= 0.111 Angle : 0.582 5.508 7813 Z= 0.271 Chirality : 0.035 0.126 883 Planarity : 0.003 0.024 883 Dihedral : 23.104 173.441 1809 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.17 % Allowed : 23.03 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.35), residues: 621 helix: 1.23 (0.30), residues: 326 sheet: -0.46 (1.06), residues: 24 loop : 0.14 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.011 0.001 TYR D 197 PHE 0.011 0.001 PHE C 208 TRP 0.011 0.001 TRP C 259 HIS 0.005 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 5701) covalent geometry : angle 0.58242 / 0.27 ( 7813) hydrogen bonds : bond 0.03294 / 2.20 ( 229) hydrogen bonds : angle 3.90019 / 2.80 ( 651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 LEU cc_start: 0.7965 (mp) cc_final: 0.7728 (mt) REVERT: C 238 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7686 (mt) REVERT: D 146 MET cc_start: 0.6679 (tpt) cc_final: 0.6308 (tpp) REVERT: D 268 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7059 (mp0) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.0711 time to fit residues: 6.3715 Evaluate side-chains 66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 268 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: [43, 31, 22, 32, 29, 24, 10, 17, 8, 1, 11] chunk 43 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.231707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184997 restraints weight = 6476.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185788 restraints weight = 5917.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186610 restraints weight = 5197.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.186995 restraints weight = 4789.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.189766 restraints weight = 4208.128| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5701 Z= 0.117 Angle : 0.586 5.715 7813 Z= 0.273 Chirality : 0.035 0.128 883 Planarity : 0.003 0.024 883 Dihedral : 23.117 173.931 1809 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.17 % Allowed : 23.23 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.35), residues: 621 helix: 1.19 (0.30), residues: 326 sheet: -0.46 (1.05), residues: 24 loop : 0.16 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.013 0.002 TYR C 207 PHE 0.007 0.001 PHE C 208 TRP 0.011 0.001 TRP C 259 HIS 0.004 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5701) covalent geometry : angle 0.58583 / 0.27 ( 7813) hydrogen bonds : bond 0.03392 / 2.28 ( 229) hydrogen bonds : angle 3.94729 / 2.82 ( 651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1094.12 seconds wall clock time: 19 minutes 37.17 seconds (1177.17 seconds total)