Starting phenix.real_space_refine on Thu Sep 10 21:56:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyy_30019/09_2026/6lyy_30019.map" } resolution = 3.2 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= 0.007 sd= 0.120 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 S 26 5.16 5 C 2670 2.51 5 N 694 2.21 5 O 711 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4104 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2902 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1167 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 681 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 7, 'HIS:plan': 3, 'ARG:plan': 6, 'TRP:plan': 4, 'GLN:plan1': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 277 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EY0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.04, per 1000 atoms: 0.25 Number of scatterers: 4104 At special positions: 0 Unit cell: (104.736, 62.187, 120.01, 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 26 16.00 F 3 9.00 O 711 8.00 N 694 7.00 C 2670 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: 0.32 Conformation dependent library (CDL) restraints added in 133.0 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 64.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 removed outlier: 4.495A pdb=" N ILE A 24 " --> pdb=" O TRP A 20 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 55 through 83 removed outlier: 4.844A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 108 through 139 Proline residue: A 130 - end of helix removed outlier: 3.505A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.564A pdb=" N ALA A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.301A pdb=" N ALA A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 194 removed outlier: 4.028A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.315A pdb=" N GLY A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 294 through 322 removed outlier: 3.777A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.657A pdb=" N THR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 removed outlier: 4.227A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 383 removed outlier: 4.608A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.870A pdb=" N VAL A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.807A pdb=" N LEU A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 440 removed outlier: 4.164A pdb=" N TYR A 423 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 4.280A pdb=" N ASN A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 205 through 234 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 235 through 238 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 32 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.066A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 115 removed outlier: 3.766A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 864 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: 0.69 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 643 1.31 - 1.43: 1151 1.43 - 1.56: 2349 1.56 - 1.68: 13 1.68 - 1.81: 40 Bond restraints: 4196 Sorted by residual: bond pdb=" C30 EY0 A 601 " pdb=" C31 EY0 A 601 " ideal model delta sigma weight residual 1.532 1.323 0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C30 EY0 A 601 " pdb=" O29 EY0 A 601 " ideal model delta sigma weight residual 1.418 1.610 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" C4 EY0 A 601 " pdb=" O10 EY0 A 601 " ideal model delta sigma weight residual 1.218 1.407 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C27 EY0 A 601 " pdb=" N28 EY0 A 601 " ideal model delta sigma weight residual 1.334 1.481 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C32 EY0 A 601 " pdb=" N28 EY0 A 601 " ideal model delta sigma weight residual 1.450 1.557 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 4191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 5297 2.07 - 4.14: 349 4.14 - 6.20: 73 6.20 - 8.27: 12 8.27 - 10.34: 5 Bond angle restraints: 5736 Sorted by residual: angle pdb=" OG1 THR A 108 " pdb=" CB THR A 108 " pdb=" CG2 THR A 108 " ideal model delta sigma weight residual 109.30 119.64 -10.34 2.00e+00 2.50e-01 2.67e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.98 -6.86 1.34e+00 5.57e-01 2.62e+01 angle pdb=" C THR B 28 " pdb=" CA THR B 28 " pdb=" CB THR B 28 " ideal model delta sigma weight residual 109.51 117.99 -8.48 1.71e+00 3.42e-01 2.46e+01 angle pdb=" CA THR A 108 " pdb=" CB THR A 108 " pdb=" CG2 THR A 108 " ideal model delta sigma weight residual 110.50 118.78 -8.28 1.70e+00 3.46e-01 2.37e+01 angle pdb=" C GLY B 58 " pdb=" N GLY B 59 " pdb=" CA GLY B 59 " ideal model delta sigma weight residual 122.47 126.79 -4.32 8.90e-01 1.26e+00 2.36e+01 ... (remaining 5731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 2113 14.71 - 29.42: 189 29.42 - 44.13: 56 44.13 - 58.84: 10 58.84 - 73.55: 5 Dihedral angle restraints: 2373 sinusoidal: 692 harmonic: 1681 Sorted by residual: dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.08 17.08 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.14 -15.74 0 2.50e+00 1.60e-01 3.97e+01 dihedral pdb=" C VAL B 61 " pdb=" N VAL B 61 " pdb=" CA VAL B 61 " pdb=" CB VAL B 61 " ideal model delta harmonic sigma weight residual -122.00 -136.20 14.20 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 2370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 655 0.260 - 0.520: 14 0.520 - 0.781: 2 0.781 - 1.041: 0 1.041 - 1.301: 1 Chirality restraints: 672 Sorted by residual: chirality pdb=" CB THR A 108 " pdb=" CA THR A 108 " pdb=" OG1 THR A 108 " pdb=" CG2 THR A 108 " both_signs ideal model delta sigma weight residual False 2.55 1.25 1.30 2.00e-01 2.50e+01 4.23e+01 chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 669 not shown) Planarity restraints: 727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.013 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C GLY B 103 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 104 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 55 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C TRP B 55 " 0.042 2.00e-02 2.50e+03 pdb=" O TRP B 55 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 323 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 324 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.029 5.00e-02 4.00e+02 ... (remaining 724 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 122 2.70 - 3.25: 4397 3.25 - 3.80: 6262 3.80 - 4.35: 7509 4.35 - 4.90: 12310 Nonbonded interactions: 30600 Sorted by model distance: nonbonded pdb=" O THR A 351 " pdb=" OG1 THR A 352 " model vdw 2.152 3.040 nonbonded pdb=" ND1 HIS B 115 " pdb=" NH2 ARG B 203 " model vdw 2.217 3.200 nonbonded pdb=" CD2 LEU A 281 " pdb=" F24 EY0 A 601 " model vdw 2.269 3.410 nonbonded pdb=" O GLY A 173 " pdb=" OG SER A 177 " model vdw 2.333 3.040 nonbonded pdb=" O GLY A 73 " pdb=" OG SER A 76 " model vdw 2.335 3.040 ... (remaining 30595 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.660 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 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 : 0.010 0.209 4196 Z= 0.606 Angle : 1.163 10.338 5736 Z= 0.739 Chirality : 0.100 1.301 672 Planarity : 0.005 0.052 727 Dihedral : 13.410 73.546 1305 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.90 % Allowed : 5.39 % Favored : 93.71 % Cbeta Deviations : 1.69 % Peptide Plane: Cis-proline : 7.41 % 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: -3.75 (0.30), residues: 591 helix: -2.37 (0.23), residues: 348 sheet: -0.47 (0.50), residues: 104 loop : -3.81 (0.39), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 175 TYR 0.012 0.002 TYR A 140 PHE 0.024 0.002 PHE A 27 TRP 0.013 0.001 TRP A 174 HIS 0.001 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.61 ( 4196) covalent geometry : angle 1.16337 / 0.74 ( 5736) hydrogen bonds : bond 0.14751 / 9.19 ( 304) hydrogen bonds : angle 6.94867 / 4.99 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.145 Fit side-chains REVERT: A 95 LEU cc_start: 0.6292 (tp) cc_final: 0.6014 (tp) REVERT: A 318 LEU cc_start: 0.8499 (tp) cc_final: 0.8236 (tt) REVERT: A 418 ASP cc_start: 0.8128 (t70) cc_final: 0.7417 (t70) outliers start: 3 outliers final: 0 residues processed: 72 average time/residue: 0.0774 time to fit residues: 6.9450 Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 270 ASN A 340 ASN B 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.239347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.207600 restraints weight = 6529.126| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.87 r_work: 0.4263 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4196 Z= 0.158 Angle : 0.685 6.305 5736 Z= 0.350 Chirality : 0.043 0.157 672 Planarity : 0.004 0.035 727 Dihedral : 4.974 42.591 635 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.19 % Allowed : 11.68 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.40 (0.35), residues: 591 helix: -0.53 (0.28), residues: 349 sheet: 0.27 (0.51), residues: 110 loop : -2.72 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 175 TYR 0.012 0.001 TYR A 113 PHE 0.019 0.002 PHE A 27 TRP 0.038 0.002 TRP A 174 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 4196) covalent geometry : angle 0.68476 / 0.35 ( 5736) hydrogen bonds : bond 0.05203 / 3.18 ( 304) hydrogen bonds : angle 5.06857 / 3.60 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.140 Fit side-chains REVERT: A 95 LEU cc_start: 0.7086 (tp) cc_final: 0.6814 (tp) REVERT: A 151 MET cc_start: 0.7559 (mmm) cc_final: 0.7213 (mtm) REVERT: A 187 ASN cc_start: 0.8164 (t0) cc_final: 0.7921 (t0) REVERT: A 274 PHE cc_start: 0.7924 (m-80) cc_final: 0.7369 (t80) REVERT: A 282 VAL cc_start: 0.8936 (p) cc_final: 0.8594 (m) REVERT: A 318 LEU cc_start: 0.8437 (tp) cc_final: 0.8230 (tt) outliers start: 14 outliers final: 6 residues processed: 82 average time/residue: 0.0552 time to fit residues: 6.0436 Evaluate side-chains 74 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 322 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.238082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.206217 restraints weight = 6338.106| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 3.04 r_work: 0.4244 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4196 Z= 0.140 Angle : 0.622 7.184 5736 Z= 0.315 Chirality : 0.042 0.145 672 Planarity : 0.004 0.039 727 Dihedral : 4.632 40.489 635 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.89 % Allowed : 14.37 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.48 (0.36), residues: 591 helix: 0.15 (0.29), residues: 349 sheet: 0.55 (0.51), residues: 112 loop : -2.14 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.013 0.001 TYR A 113 PHE 0.021 0.001 PHE A 274 TRP 0.014 0.001 TRP A 174 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 4196) covalent geometry : angle 0.62226 / 0.31 ( 5736) hydrogen bonds : bond 0.04572 / 2.81 ( 304) hydrogen bonds : angle 4.71038 / 3.33 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.158 Fit side-chains REVERT: A 138 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: A 196 ARG cc_start: 0.7598 (mtm180) cc_final: 0.7283 (mtm180) REVERT: A 282 VAL cc_start: 0.9074 (p) cc_final: 0.8676 (m) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 0.0572 time to fit residues: 6.5296 Evaluate side-chains 73 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 322 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.231677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.199647 restraints weight = 6200.851| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.98 r_work: 0.4184 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4196 Z= 0.140 Angle : 0.627 9.725 5736 Z= 0.315 Chirality : 0.042 0.139 672 Planarity : 0.004 0.042 727 Dihedral : 4.519 34.472 635 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.99 % Allowed : 15.87 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.07 (0.37), residues: 591 helix: 0.46 (0.29), residues: 352 sheet: 1.14 (0.54), residues: 98 loop : -2.09 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.013 0.001 TYR A 287 PHE 0.019 0.002 PHE A 27 TRP 0.012 0.002 TRP A 174 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 4196) covalent geometry : angle 0.62709 / 0.32 ( 5736) hydrogen bonds : bond 0.04513 / 2.78 ( 304) hydrogen bonds : angle 4.60463 / 3.24 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.159 Fit side-chains REVERT: A 138 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7396 (m-80) outliers start: 20 outliers final: 10 residues processed: 94 average time/residue: 0.0429 time to fit residues: 5.6626 Evaluate side-chains 84 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.229619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.199117 restraints weight = 6140.322| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.84 r_work: 0.4185 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4196 Z= 0.136 Angle : 0.606 7.616 5736 Z= 0.306 Chirality : 0.042 0.144 672 Planarity : 0.004 0.048 727 Dihedral : 4.388 27.298 635 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.99 % Allowed : 20.36 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.07 (0.37), residues: 591 helix: 0.61 (0.29), residues: 353 sheet: 1.05 (0.53), residues: 98 loop : -2.02 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.010 0.001 TYR A 287 PHE 0.021 0.001 PHE A 27 TRP 0.009 0.001 TRP A 174 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 4196) covalent geometry : angle 0.60552 / 0.31 ( 5736) hydrogen bonds : bond 0.04457 / 2.73 ( 304) hydrogen bonds : angle 4.54652 / 3.20 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.124 Fit side-chains REVERT: A 138 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: A 274 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7240 (t80) REVERT: A 412 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6537 (mp) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.0398 time to fit residues: 5.3214 Evaluate side-chains 89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 0.0030 chunk 32 optimal weight: 0.4980 chunk 35 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 overall best weight: 0.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.235747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.205871 restraints weight = 6413.327| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.87 r_work: 0.4251 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4196 Z= 0.118 Angle : 0.606 8.543 5736 Z= 0.294 Chirality : 0.041 0.128 672 Planarity : 0.004 0.040 727 Dihedral : 4.198 24.166 635 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.09 % Allowed : 20.96 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.53 (0.37), residues: 591 helix: 0.97 (0.30), residues: 352 sheet: 1.14 (0.53), residues: 103 loop : -1.85 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.010 0.001 TYR A 113 PHE 0.021 0.001 PHE A 27 TRP 0.013 0.001 TRP A 18 HIS 0.001 0.000 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 4196) covalent geometry : angle 0.60618 / 0.29 ( 5736) hydrogen bonds : bond 0.03687 / 2.29 ( 304) hydrogen bonds : angle 4.23835 / 2.97 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.140 Fit side-chains REVERT: A 69 MET cc_start: 0.7633 (ttm) cc_final: 0.7421 (ttp) REVERT: A 138 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: A 194 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 274 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 412 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6250 (mp) REVERT: B 201 ARG cc_start: 0.5450 (ttt180) cc_final: 0.4993 (ttp-170) outliers start: 17 outliers final: 8 residues processed: 89 average time/residue: 0.0423 time to fit residues: 5.4220 Evaluate side-chains 87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4605 r_free = 0.4605 target = 0.229729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.199046 restraints weight = 6357.009| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.95 r_work: 0.4190 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4196 Z= 0.132 Angle : 0.614 7.901 5736 Z= 0.306 Chirality : 0.042 0.143 672 Planarity : 0.004 0.048 727 Dihedral : 4.201 24.905 635 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.09 % Allowed : 22.75 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.50 (0.37), residues: 591 helix: 0.89 (0.29), residues: 353 sheet: 1.34 (0.53), residues: 100 loop : -1.84 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.008 0.001 TYR A 113 PHE 0.020 0.001 PHE A 27 TRP 0.008 0.001 TRP A 18 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4196) covalent geometry : angle 0.61416 / 0.31 ( 5736) hydrogen bonds : bond 0.04277 / 2.64 ( 304) hydrogen bonds : angle 4.37766 / 3.08 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.143 Fit side-chains REVERT: A 18 TRP cc_start: 0.6760 (OUTLIER) cc_final: 0.5244 (t60) REVERT: A 138 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: A 274 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7349 (t80) REVERT: A 412 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6440 (mp) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 0.0437 time to fit residues: 6.0033 Evaluate side-chains 95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.0020 chunk 28 optimal weight: 0.0010 chunk 11 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.231833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.201391 restraints weight = 6269.756| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 2.85 r_work: 0.4234 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4196 Z= 0.120 Angle : 0.621 9.222 5736 Z= 0.303 Chirality : 0.041 0.131 672 Planarity : 0.004 0.044 727 Dihedral : 4.149 25.136 635 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.29 % Allowed : 22.16 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.72 (0.37), residues: 591 helix: 1.07 (0.30), residues: 352 sheet: 1.48 (0.53), residues: 100 loop : -1.78 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.012 0.001 TYR A 419 PHE 0.022 0.001 PHE A 27 TRP 0.010 0.001 TRP A 18 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 4196) covalent geometry : angle 0.62141 / 0.30 ( 5736) hydrogen bonds : bond 0.03921 / 2.42 ( 304) hydrogen bonds : angle 4.20711 / 2.95 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.148 Fit side-chains REVERT: A 18 TRP cc_start: 0.6709 (OUTLIER) cc_final: 0.5262 (t60) REVERT: A 138 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7239 (m-80) REVERT: A 194 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8382 (tp) REVERT: A 274 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7355 (t80) REVERT: B 201 ARG cc_start: 0.5678 (ttt180) cc_final: 0.5150 (ttp-170) outliers start: 21 outliers final: 12 residues processed: 89 average time/residue: 0.0418 time to fit residues: 5.3516 Evaluate side-chains 93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 433 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4563 r_free = 0.4563 target = 0.225070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.194808 restraints weight = 6303.480| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.89 r_work: 0.4168 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4196 Z= 0.158 Angle : 0.660 9.016 5736 Z= 0.330 Chirality : 0.043 0.148 672 Planarity : 0.004 0.053 727 Dihedral : 4.368 26.385 635 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.79 % Allowed : 23.95 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.45 (0.36), residues: 591 helix: 0.82 (0.29), residues: 353 sheet: 1.14 (0.51), residues: 108 loop : -1.78 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.009 0.001 TYR A 331 PHE 0.019 0.001 PHE A 27 TRP 0.008 0.001 TRP A 424 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 4196) covalent geometry : angle 0.65995 / 0.33 ( 5736) hydrogen bonds : bond 0.04806 / 2.97 ( 304) hydrogen bonds : angle 4.54637 / 3.20 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.102 Fit side-chains REVERT: A 18 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.5469 (t60) REVERT: A 46 GLU cc_start: 0.8352 (tp30) cc_final: 0.8035 (tp30) REVERT: A 138 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: A 274 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7380 (t80) REVERT: B 201 ARG cc_start: 0.5867 (ttt180) cc_final: 0.5310 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.0428 time to fit residues: 5.4617 Evaluate side-chains 93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 50.0000 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4567 r_free = 0.4567 target = 0.226932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.196323 restraints weight = 6272.216| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.95 r_work: 0.4160 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4196 Z= 0.128 Angle : 0.653 10.944 5736 Z= 0.318 Chirality : 0.041 0.139 672 Planarity : 0.004 0.050 727 Dihedral : 4.238 26.050 635 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.49 % Allowed : 24.25 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.74 (0.37), residues: 591 helix: 1.01 (0.29), residues: 353 sheet: 1.26 (0.52), residues: 108 loop : -1.50 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.015 0.001 TYR A 359 PHE 0.022 0.001 PHE A 27 TRP 0.010 0.001 TRP A 18 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 4196) covalent geometry : angle 0.65295 / 0.32 ( 5736) hydrogen bonds : bond 0.04218 / 2.60 ( 304) hydrogen bonds : angle 4.30241 / 3.01 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.166 Fit side-chains REVERT: A 18 TRP cc_start: 0.7075 (OUTLIER) cc_final: 0.5673 (t60) REVERT: A 138 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: A 274 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7356 (t80) REVERT: B 201 ARG cc_start: 0.5734 (ttt180) cc_final: 0.5250 (ttp-170) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.0459 time to fit residues: 5.8335 Evaluate side-chains 94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.224654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194153 restraints weight = 6366.727| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.99 r_work: 0.4138 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4196 Z= 0.140 Angle : 0.649 10.078 5736 Z= 0.320 Chirality : 0.042 0.137 672 Planarity : 0.004 0.050 727 Dihedral : 4.283 26.909 635 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.79 % Allowed : 23.65 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.81 (0.37), residues: 591 helix: 1.01 (0.29), residues: 352 sheet: 1.59 (0.53), residues: 107 loop : -1.55 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.015 0.001 TYR A 359 PHE 0.021 0.001 PHE A 27 TRP 0.009 0.001 TRP A 18 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4196) covalent geometry : angle 0.64899 / 0.32 ( 5736) hydrogen bonds : bond 0.04420 / 2.73 ( 304) hydrogen bonds : angle 4.36824 / 3.06 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.29 seconds wall clock time: 22 minutes 47.20 seconds (1367.20 seconds total)