Starting phenix.real_space_refine on Thu Mar 6 01:37:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3b_45164/03_2025/9c3b_45164.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3b_45164/03_2025/9c3b_45164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c3b_45164/03_2025/9c3b_45164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3b_45164/03_2025/9c3b_45164.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3b_45164/03_2025/9c3b_45164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3b_45164/03_2025/9c3b_45164.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2731 2.51 5 N 742 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4329 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3234 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 13, 'TRANS': 431} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1095 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.57, per 1000 atoms: 1.52 Number of scatterers: 4329 At special positions: 0 Unit cell: (108.528, 110.16, 84.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 846 8.00 N 742 7.00 C 2731 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: 1.00 Conformation dependent library (CDL) restraints added in 545.5 milliseconds 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1096 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 32.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 removed outlier: 4.015A pdb=" N ASP A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.075A pdb=" N GLY A 106 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.001A pdb=" N SER A 152 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.640A pdb=" N TYR A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.848A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.588A pdb=" N GLN A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.647A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.577A pdb=" N TYR A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 345 through 369 removed outlier: 3.515A pdb=" N ASN A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 399 removed outlier: 3.570A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.871A pdb=" N VAL A 415 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.594A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.547A pdb=" N VAL B 12 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 85 removed outlier: 3.779A pdb=" N ALA B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.441A pdb=" N GLY A 77 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE A 27 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 202 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ALA A 229 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ALA A 204 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE A 326 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 325 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 293 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 146 removed outlier: 6.005A pdb=" N LYS A 159 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N MET A 81 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 408 removed outlier: 6.692A pdb=" N ILE A 433 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N HIS A 431 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 407 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR A 429 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.387A pdb=" N CYS B 14 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER B 93 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 110 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 97 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA B 106 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B 138 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 109 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 136 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.817A pdb=" N ILE B 131 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 159 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.20 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: 1444 1.34 - 1.46: 655 1.46 - 1.57: 2287 1.57 - 1.69: 1 1.69 - 1.80: 16 Bond restraints: 4403 Sorted by residual: bond pdb=" CA SER B 71 " pdb=" CB SER B 71 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.58e-02 4.01e+03 1.10e+01 bond pdb=" CB PRO A 136 " pdb=" CG PRO A 136 " ideal model delta sigma weight residual 1.492 1.644 -0.152 5.00e-02 4.00e+02 9.25e+00 bond pdb=" N ILE A 5 " pdb=" CA ILE A 5 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" CA SER A 357 " pdb=" CB SER A 357 " ideal model delta sigma weight residual 1.530 1.480 0.049 1.69e-02 3.50e+03 8.53e+00 bond pdb=" N PHE A 34 " pdb=" CA PHE A 34 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.11e+00 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 5890 2.89 - 5.78: 108 5.78 - 8.67: 6 8.67 - 11.56: 1 11.56 - 14.45: 1 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" CD PRO A 136 " ideal model delta sigma weight residual 112.00 97.55 14.45 1.40e+00 5.10e-01 1.07e+02 angle pdb=" N PRO A 88 " pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " ideal model delta sigma weight residual 103.25 94.60 8.65 1.05e+00 9.07e-01 6.79e+01 angle pdb=" N LEU A 355 " pdb=" CA LEU A 355 " pdb=" C LEU A 355 " ideal model delta sigma weight residual 111.07 105.68 5.39 1.07e+00 8.73e-01 2.54e+01 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 105.01 6.99 1.40e+00 5.10e-01 2.49e+01 angle pdb=" N THR A 147 " pdb=" CA THR A 147 " pdb=" C THR A 147 " ideal model delta sigma weight residual 111.07 106.06 5.01 1.07e+00 8.73e-01 2.19e+01 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2296 17.47 - 34.93: 259 34.93 - 52.40: 49 52.40 - 69.86: 18 69.86 - 87.33: 8 Dihedral angle restraints: 2630 sinusoidal: 931 harmonic: 1699 Sorted by residual: dihedral pdb=" CD ARG A 308 " pdb=" NE ARG A 308 " pdb=" CZ ARG A 308 " pdb=" NH1 ARG A 308 " ideal model delta sinusoidal sigma weight residual 0.00 -62.69 62.69 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CD ARG B 123 " pdb=" NE ARG B 123 " pdb=" CZ ARG B 123 " pdb=" NH1 ARG B 123 " ideal model delta sinusoidal sigma weight residual 0.00 -29.82 29.82 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CB GLU B 22 " pdb=" CG GLU B 22 " pdb=" CD GLU B 22 " pdb=" OE1 GLU B 22 " ideal model delta sinusoidal sigma weight residual 0.00 87.33 -87.33 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 2627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 546 0.051 - 0.102: 133 0.102 - 0.153: 35 0.153 - 0.203: 3 0.203 - 0.254: 2 Chirality restraints: 719 Sorted by residual: chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" C PRO A 136 " pdb=" CB PRO A 136 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASP A 427 " pdb=" N ASP A 427 " pdb=" C ASP A 427 " pdb=" CB ASP A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 716 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 308 " 0.989 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG A 308 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 308 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 308 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 308 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 123 " -0.546 9.50e-02 1.11e+02 2.45e-01 3.66e+01 pdb=" NE ARG B 123 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG B 123 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 123 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 123 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 135 " -0.070 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 136 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " -0.052 5.00e-02 4.00e+02 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 695 2.75 - 3.29: 4142 3.29 - 3.83: 6855 3.83 - 4.36: 7848 4.36 - 4.90: 13683 Nonbonded interactions: 33223 Sorted by model distance: nonbonded pdb=" OH TYR A 200 " pdb=" OD2 ASP A 353 " model vdw 2.213 3.040 nonbonded pdb=" O ALA A 267 " pdb=" N PHE A 269 " model vdw 2.302 3.120 nonbonded pdb=" OG1 THR A 80 " pdb=" OD2 ASP A 183 " model vdw 2.310 3.040 nonbonded pdb=" OG SER A 217 " pdb=" OH TYR A 256 " model vdw 2.310 3.040 nonbonded pdb=" O ASP A 52 " pdb=" OG1 THR A 55 " model vdw 2.319 3.040 ... (remaining 33218 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: 12.420 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.007 0.152 4403 Z= 0.453 Angle : 0.885 14.453 6006 Z= 0.577 Chirality : 0.049 0.254 719 Planarity : 0.020 0.443 775 Dihedral : 16.525 87.326 1534 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 1.54 % Allowed : 8.22 % Favored : 90.24 % Rotamer: Outliers : 3.24 % Allowed : 19.21 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.36), residues: 584 helix: 1.90 (0.45), residues: 139 sheet: -0.38 (0.49), residues: 122 loop : -1.98 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 199 HIS 0.002 0.001 HIS A 264 PHE 0.016 0.002 PHE A 165 TYR 0.009 0.001 TYR A 271 ARG 0.003 0.001 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6099 (ptt180) REVERT: A 419 ASP cc_start: 0.8241 (m-30) cc_final: 0.7806 (m-30) REVERT: B 53 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.5141 (mtt90) outliers start: 14 outliers final: 0 residues processed: 146 average time/residue: 0.1684 time to fit residues: 30.2412 Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 53 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN B 5 GLN B 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.072010 restraints weight = 12193.821| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.73 r_work: 0.2947 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 4403 Z= 0.247 Angle : 0.636 8.594 6006 Z= 0.334 Chirality : 0.046 0.251 719 Planarity : 0.006 0.127 775 Dihedral : 5.256 54.871 634 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.82 % Favored : 93.32 % Rotamer: Outliers : 6.71 % Allowed : 20.14 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.35), residues: 584 helix: 1.40 (0.42), residues: 158 sheet: -0.21 (0.51), residues: 110 loop : -2.03 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 65 HIS 0.003 0.001 HIS A 265 PHE 0.008 0.002 PHE A 51 TYR 0.018 0.001 TYR A 200 ARG 0.007 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8379 (m-10) cc_final: 0.7937 (m-10) REVERT: A 155 MET cc_start: 0.6872 (tpt) cc_final: 0.5785 (tmm) REVERT: A 303 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: A 308 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7210 (mtm180) REVERT: A 332 VAL cc_start: 0.8313 (t) cc_final: 0.7993 (p) REVERT: A 368 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8939 (tt) REVERT: A 369 ASN cc_start: 0.9119 (m-40) cc_final: 0.8882 (m110) REVERT: B 81 LYS cc_start: 0.8877 (mttt) cc_final: 0.8662 (ttpp) REVERT: B 120 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 123 ARG cc_start: 0.6231 (mtm-85) cc_final: 0.5686 (mtt90) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.1335 time to fit residues: 17.5176 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.070208 restraints weight = 12065.322| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.66 r_work: 0.2915 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4403 Z= 0.296 Angle : 0.621 6.280 6006 Z= 0.333 Chirality : 0.046 0.182 719 Planarity : 0.006 0.112 775 Dihedral : 4.962 49.847 630 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.02 % Favored : 92.12 % Rotamer: Outliers : 4.40 % Allowed : 22.92 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.35), residues: 584 helix: 1.66 (0.42), residues: 157 sheet: -0.14 (0.51), residues: 110 loop : -1.94 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.001 0.001 HIS A 264 PHE 0.011 0.001 PHE A 51 TYR 0.011 0.001 TYR B 98 ARG 0.004 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8622 (m-10) cc_final: 0.8130 (m-10) REVERT: A 155 MET cc_start: 0.6991 (tpt) cc_final: 0.5695 (tmm) REVERT: A 308 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7336 (mtm180) REVERT: B 120 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 123 ARG cc_start: 0.5863 (mtm-85) cc_final: 0.5249 (mpt180) outliers start: 19 outliers final: 13 residues processed: 65 average time/residue: 0.1697 time to fit residues: 14.1977 Evaluate side-chains 56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.065025 restraints weight = 12432.468| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.60 r_work: 0.2808 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 4403 Z= 0.481 Angle : 0.701 5.690 6006 Z= 0.373 Chirality : 0.049 0.206 719 Planarity : 0.006 0.105 775 Dihedral : 5.297 46.097 630 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.19 % Favored : 91.95 % Rotamer: Outliers : 4.86 % Allowed : 22.45 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.35), residues: 584 helix: 1.51 (0.40), residues: 157 sheet: -0.28 (0.50), residues: 110 loop : -2.05 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 65 HIS 0.004 0.002 HIS A 264 PHE 0.009 0.002 PHE A 211 TYR 0.011 0.002 TYR A 377 ARG 0.010 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7414 (tpt) cc_final: 0.6281 (tmm) REVERT: A 308 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7608 (mtp180) REVERT: B 89 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8303 (mp0) REVERT: B 120 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8029 (tm-30) outliers start: 21 outliers final: 15 residues processed: 57 average time/residue: 0.1411 time to fit residues: 10.8365 Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067231 restraints weight = 12336.679| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.59 r_work: 0.2858 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4403 Z= 0.237 Angle : 0.550 5.374 6006 Z= 0.296 Chirality : 0.044 0.185 719 Planarity : 0.005 0.100 775 Dihedral : 4.821 44.198 630 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.62 % Favored : 94.52 % Rotamer: Outliers : 3.47 % Allowed : 23.15 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.35), residues: 584 helix: 1.92 (0.42), residues: 157 sheet: -0.10 (0.52), residues: 104 loop : -2.03 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.002 0.001 HIS A 264 PHE 0.006 0.001 PHE A 211 TYR 0.007 0.001 TYR A 271 ARG 0.002 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.467 Fit side-chains REVERT: A 155 MET cc_start: 0.7499 (tpt) cc_final: 0.6405 (tmm) REVERT: A 308 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7479 (mtm180) REVERT: B 81 LYS cc_start: 0.9265 (ttpp) cc_final: 0.9051 (tttm) REVERT: B 89 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8322 (mp0) REVERT: B 120 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8055 (tm-30) outliers start: 15 outliers final: 7 residues processed: 54 average time/residue: 0.1626 time to fit residues: 11.4641 Evaluate side-chains 49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067084 restraints weight = 12140.255| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.56 r_work: 0.2847 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4403 Z= 0.243 Angle : 0.557 5.312 6006 Z= 0.299 Chirality : 0.044 0.188 719 Planarity : 0.005 0.097 775 Dihedral : 4.748 43.233 630 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.31 % Favored : 93.84 % Rotamer: Outliers : 3.94 % Allowed : 21.99 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.35), residues: 584 helix: 1.98 (0.42), residues: 157 sheet: 0.05 (0.53), residues: 102 loop : -2.04 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 199 HIS 0.002 0.001 HIS A 264 PHE 0.005 0.001 PHE A 430 TYR 0.007 0.001 TYR B 98 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.503 Fit side-chains REVERT: A 155 MET cc_start: 0.7636 (tpt) cc_final: 0.6474 (tmm) REVERT: A 308 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7616 (mtp180) REVERT: B 89 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8321 (mp0) REVERT: B 120 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 123 ARG cc_start: 0.6082 (OUTLIER) cc_final: 0.3858 (mtm-85) outliers start: 17 outliers final: 11 residues processed: 55 average time/residue: 0.1668 time to fit residues: 12.1841 Evaluate side-chains 52 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 50.0000 chunk 34 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.065390 restraints weight = 12321.879| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.59 r_work: 0.2816 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.7556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4403 Z= 0.349 Angle : 0.608 5.459 6006 Z= 0.325 Chirality : 0.046 0.192 719 Planarity : 0.006 0.097 775 Dihedral : 4.879 41.558 630 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.65 % Favored : 93.49 % Rotamer: Outliers : 3.94 % Allowed : 22.92 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.35), residues: 584 helix: 1.89 (0.41), residues: 158 sheet: -0.06 (0.53), residues: 104 loop : -1.99 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 199 HIS 0.004 0.001 HIS A 264 PHE 0.017 0.001 PHE A 227 TYR 0.009 0.001 TYR B 98 ARG 0.002 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7672 (tpt) cc_final: 0.6474 (tmm) REVERT: A 308 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7573 (mtp180) REVERT: B 73 GLN cc_start: 0.9407 (OUTLIER) cc_final: 0.9077 (mt0) REVERT: B 89 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8308 (mp0) REVERT: B 120 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 123 ARG cc_start: 0.5806 (OUTLIER) cc_final: 0.3790 (mtm-85) outliers start: 17 outliers final: 11 residues processed: 49 average time/residue: 0.1500 time to fit residues: 9.8465 Evaluate side-chains 47 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 40.0000 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067823 restraints weight = 12014.124| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.62 r_work: 0.2866 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.7626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4403 Z= 0.191 Angle : 0.544 5.228 6006 Z= 0.293 Chirality : 0.044 0.182 719 Planarity : 0.005 0.096 775 Dihedral : 4.529 38.909 630 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.79 % Favored : 94.35 % Rotamer: Outliers : 3.01 % Allowed : 24.07 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.35), residues: 584 helix: 2.01 (0.42), residues: 158 sheet: -0.19 (0.51), residues: 110 loop : -1.88 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 354 HIS 0.002 0.001 HIS A 264 PHE 0.015 0.001 PHE A 227 TYR 0.007 0.001 TYR B 139 ARG 0.002 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7668 (tpt) cc_final: 0.6519 (tmm) REVERT: A 308 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7610 (mtp180) REVERT: B 89 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8275 (mp0) REVERT: B 120 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8110 (tm-30) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.1492 time to fit residues: 10.3660 Evaluate side-chains 49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.084120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.065125 restraints weight = 12247.834| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.61 r_work: 0.2827 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.7822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 4403 Z= 0.471 Angle : 0.653 5.523 6006 Z= 0.348 Chirality : 0.047 0.192 719 Planarity : 0.006 0.097 775 Dihedral : 4.883 38.834 630 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.51 % Favored : 92.81 % Rotamer: Outliers : 4.40 % Allowed : 21.30 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.35), residues: 584 helix: 1.89 (0.41), residues: 158 sheet: -0.45 (0.50), residues: 112 loop : -1.85 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 65 HIS 0.005 0.002 HIS A 264 PHE 0.011 0.001 PHE A 227 TYR 0.009 0.002 TYR A 377 ARG 0.003 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7777 (tpt) cc_final: 0.6641 (tmm) REVERT: A 308 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7577 (mtp180) REVERT: B 89 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8392 (mp0) REVERT: B 120 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: B 123 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.3825 (mtm-85) outliers start: 19 outliers final: 15 residues processed: 48 average time/residue: 0.1571 time to fit residues: 10.2004 Evaluate side-chains 49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 50.0000 chunk 13 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.067005 restraints weight = 11975.523| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.60 r_work: 0.2867 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.7876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4403 Z= 0.245 Angle : 0.571 5.470 6006 Z= 0.307 Chirality : 0.044 0.184 719 Planarity : 0.005 0.097 775 Dihedral : 4.609 37.807 630 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.97 % Favored : 94.35 % Rotamer: Outliers : 3.47 % Allowed : 22.45 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.36), residues: 584 helix: 2.05 (0.41), residues: 158 sheet: -0.35 (0.51), residues: 112 loop : -1.81 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 264 PHE 0.015 0.001 PHE A 227 TYR 0.007 0.001 TYR B 139 ARG 0.002 0.000 ARG A 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7798 (tpt) cc_final: 0.6644 (tmm) REVERT: A 308 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7601 (mtp180) REVERT: B 89 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8382 (mp0) REVERT: B 120 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 123 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.3842 (mtm-85) outliers start: 15 outliers final: 12 residues processed: 49 average time/residue: 0.1501 time to fit residues: 9.8558 Evaluate side-chains 51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 chunk 37 optimal weight: 5.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.068246 restraints weight = 12119.273| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.61 r_work: 0.2889 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.7968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4403 Z= 0.203 Angle : 0.542 5.346 6006 Z= 0.291 Chirality : 0.043 0.184 719 Planarity : 0.005 0.097 775 Dihedral : 4.318 34.968 630 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.82 % Favored : 93.49 % Rotamer: Outliers : 2.55 % Allowed : 23.61 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.36), residues: 584 helix: 2.18 (0.41), residues: 159 sheet: -0.39 (0.50), residues: 112 loop : -1.77 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 354 HIS 0.002 0.001 HIS A 264 PHE 0.014 0.001 PHE A 227 TYR 0.006 0.001 TYR A 271 ARG 0.002 0.000 ARG A 258 =============================================================================== Job complete usr+sys time: 3651.73 seconds wall clock time: 64 minutes 26.89 seconds (3866.89 seconds total)