Starting phenix.real_space_refine on Tue Feb 11 06:01:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3b_45164/02_2025/9c3b_45164.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3b_45164/02_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_45164/02_2025/9c3b_45164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3b_45164/02_2025/9c3b_45164.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3b_45164/02_2025/9c3b_45164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3b_45164/02_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-5592/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: 6.39, per 1000 atoms: 1.48 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: 1.02 Conformation dependent library (CDL) restraints added in 574.4 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: 0.58 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: 1.10 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: 11.320 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.060 Find NCS groups from input model: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.480 ------------------------------------------------------------------------------- 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 : 0.461 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: 0.1725 time to fit residues: 31.0957 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 : 0.519 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.072011 restraints weight = 12193.819| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.73 r_work: 0.2947 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.523 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8377 (m-10) cc_final: 0.7937 (m-10) REVERT: A 155 MET cc_start: 0.6871 (tpt) cc_final: 0.5783 (tmm) REVERT: A 303 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: A 308 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7210 (mtm180) REVERT: A 332 VAL cc_start: 0.8313 (t) cc_final: 0.7995 (p) REVERT: A 368 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8940 (tt) REVERT: A 369 ASN cc_start: 0.9118 (m-40) cc_final: 0.8881 (m110) REVERT: B 81 LYS cc_start: 0.8877 (mttt) cc_final: 0.8664 (ttpp) REVERT: B 120 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8215 (tm-30) REVERT: B 123 ARG cc_start: 0.6234 (mtm-85) cc_final: 0.5687 (mtt90) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.1406 time to fit residues: 18.4458 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 : 0.502 ------------------------------------------------------------------------------- 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: 8.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 0.0000 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.088250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.069774 restraints weight = 12087.282| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.64 r_work: 0.2904 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 4403 Z= 0.319 Angle : 0.644 6.444 6006 Z= 0.347 Chirality : 0.046 0.188 719 Planarity : 0.006 0.112 775 Dihedral : 5.066 49.726 630 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.85 % Favored : 92.29 % Rotamer: Outliers : 4.63 % Allowed : 23.38 % Favored : 71.99 % 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: -0.87 (0.35), residues: 584 helix: 1.59 (0.42), residues: 157 sheet: -0.15 (0.50), residues: 110 loop : -1.96 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 65 HIS 0.002 0.001 HIS A 264 PHE 0.011 0.001 PHE A 51 TYR 0.012 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 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7068 (tpt) cc_final: 0.5776 (tmm) REVERT: A 308 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7107 (mtm180) REVERT: B 120 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 123 ARG cc_start: 0.5724 (mtm-85) cc_final: 0.5115 (mpt180) outliers start: 20 outliers final: 13 residues processed: 66 average time/residue: 0.1616 time to fit residues: 13.8202 Evaluate side-chains 54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066866 restraints weight = 12275.002| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.60 r_work: 0.2847 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4403 Z= 0.323 Angle : 0.605 5.959 6006 Z= 0.322 Chirality : 0.046 0.190 719 Planarity : 0.006 0.105 775 Dihedral : 5.074 51.159 630 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.34 % Favored : 92.81 % 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: -0.76 (0.36), residues: 584 helix: 1.83 (0.42), residues: 157 sheet: -0.08 (0.51), residues: 110 loop : -2.00 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 65 HIS 0.003 0.001 HIS A 264 PHE 0.007 0.001 PHE A 211 TYR 0.008 0.001 TYR B 98 ARG 0.003 0.001 ARG B 31 *********************** 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 65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7318 (tpt) cc_final: 0.6174 (tmm) REVERT: A 308 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7798 (mtp180) REVERT: B 89 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8279 (mp0) REVERT: B 120 GLU cc_start: 0.8673 (tm-30) cc_final: 0.7999 (tm-30) outliers start: 19 outliers final: 15 residues processed: 63 average time/residue: 0.1445 time to fit residues: 12.0630 Evaluate side-chains 59 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 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 126 ASN Chi-restraints excluded: chain B residue 127 SER 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: 5.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067335 restraints weight = 12372.323| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.60 r_work: 0.2877 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.7022 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= 0.259 Angle : 0.560 5.341 6006 Z= 0.301 Chirality : 0.044 0.191 719 Planarity : 0.006 0.099 775 Dihedral : 4.852 49.391 630 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.97 % Favored : 94.18 % Rotamer: Outliers : 4.40 % Allowed : 23.15 % Favored : 72.45 % 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: -0.67 (0.35), residues: 584 helix: 2.04 (0.42), residues: 157 sheet: -0.03 (0.52), residues: 104 loop : -1.99 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.002 0.001 HIS A 264 PHE 0.006 0.001 PHE B 132 TYR 0.007 0.001 TYR A 271 ARG 0.002 0.000 ARG A 222 *********************** 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 65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.505 Fit side-chains REVERT: A 155 MET cc_start: 0.7397 (tpt) cc_final: 0.6293 (tmm) REVERT: A 218 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8724 (mm-30) REVERT: A 308 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7700 (mtp180) REVERT: B 81 LYS cc_start: 0.9230 (ttpp) cc_final: 0.9000 (tttm) REVERT: B 89 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8248 (mp0) REVERT: B 120 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8025 (tm-30) outliers start: 19 outliers final: 12 residues processed: 64 average time/residue: 0.1496 time to fit residues: 12.5703 Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 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 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.067714 restraints weight = 11996.362| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.58 r_work: 0.2880 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.7220 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= 0.265 Angle : 0.570 5.316 6006 Z= 0.305 Chirality : 0.045 0.188 719 Planarity : 0.005 0.098 775 Dihedral : 4.829 48.116 630 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.82 % Favored : 93.32 % Rotamer: Outliers : 4.17 % Allowed : 23.84 % Favored : 71.99 % 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: -0.66 (0.35), residues: 584 helix: 2.16 (0.43), residues: 157 sheet: -0.08 (0.52), residues: 104 loop : -2.03 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 65 HIS 0.003 0.001 HIS A 264 PHE 0.005 0.001 PHE B 132 TYR 0.007 0.001 TYR B 98 ARG 0.002 0.000 ARG A 79 *********************** 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 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.471 Fit side-chains REVERT: A 143 ASN cc_start: 0.8834 (m-40) cc_final: 0.8623 (m-40) REVERT: A 155 MET cc_start: 0.7579 (tpt) cc_final: 0.6442 (tmm) REVERT: A 308 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: B 81 LYS cc_start: 0.9327 (ttpp) cc_final: 0.9114 (tttm) REVERT: B 89 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8329 (mp0) REVERT: B 120 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8270 (tm-30) outliers start: 18 outliers final: 14 residues processed: 54 average time/residue: 0.1388 time to fit residues: 10.1493 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 : 0.464 ------------------------------------------------------------------------------- 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 181 THR Chi-restraints excluded: chain A residue 189 LEU 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 429 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 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 0.0050 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 48 optimal weight: 0.0370 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 50.0000 chunk 34 optimal weight: 0.9980 overall best weight: 2.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068482 restraints weight = 11975.255| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.58 r_work: 0.2899 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4403 Z= 0.214 Angle : 0.541 5.190 6006 Z= 0.291 Chirality : 0.044 0.187 719 Planarity : 0.005 0.096 775 Dihedral : 4.624 45.942 630 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.97 % Favored : 94.18 % Rotamer: Outliers : 4.17 % Allowed : 24.07 % Favored : 71.76 % 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: -0.56 (0.35), residues: 584 helix: 2.19 (0.43), residues: 158 sheet: 0.11 (0.53), residues: 102 loop : -1.99 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 65 HIS 0.002 0.001 HIS A 264 PHE 0.018 0.001 PHE A 227 TYR 0.007 0.001 TYR B 139 ARG 0.002 0.000 ARG A 79 *********************** 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 59 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7621 (tpt) cc_final: 0.6496 (tmm) REVERT: A 308 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7667 (mtp180) REVERT: B 81 LYS cc_start: 0.9254 (ttpp) cc_final: 0.8948 (tttm) REVERT: B 89 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8306 (mp0) REVERT: B 120 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8062 (tm-30) REVERT: B 123 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.3579 (mtm-85) outliers start: 18 outliers final: 12 residues processed: 57 average time/residue: 0.1400 time to fit residues: 10.6477 Evaluate side-chains 50 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 181 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 A residue 404 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 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: 9.9990 chunk 10 optimal weight: 40.0000 chunk 6 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN A 398 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.067020 restraints weight = 11928.257| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.58 r_work: 0.2867 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4403 Z= 0.302 Angle : 0.586 5.322 6006 Z= 0.314 Chirality : 0.045 0.186 719 Planarity : 0.005 0.096 775 Dihedral : 4.748 43.847 630 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.16 % Favored : 92.98 % Rotamer: Outliers : 5.09 % Allowed : 23.61 % Favored : 71.30 % 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: -0.55 (0.35), residues: 584 helix: 2.22 (0.42), residues: 158 sheet: -0.00 (0.53), residues: 102 loop : -1.94 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.003 0.001 HIS A 264 PHE 0.014 0.001 PHE A 227 TYR 0.008 0.001 TYR B 98 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 56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: A 155 MET cc_start: 0.7673 (tpt) cc_final: 0.6539 (tmm) REVERT: A 308 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7623 (mtp180) REVERT: B 120 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 123 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.3900 (mtm-85) outliers start: 22 outliers final: 17 residues processed: 53 average time/residue: 0.1476 time to fit residues: 10.5072 Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 128 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 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 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 6 GLN 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 Chi-restraints excluded: chain B residue 142 THR 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: 4.9990 chunk 32 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 394 GLN A 398 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066150 restraints weight = 12222.288| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.61 r_work: 0.2853 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4403 Z= 0.362 Angle : 0.607 5.553 6006 Z= 0.325 Chirality : 0.046 0.188 719 Planarity : 0.006 0.097 775 Dihedral : 4.797 42.889 630 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.82 % Favored : 93.49 % Rotamer: Outliers : 5.09 % Allowed : 22.92 % Favored : 71.99 % 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: -0.64 (0.35), residues: 584 helix: 2.04 (0.41), residues: 158 sheet: -0.40 (0.50), residues: 112 loop : -1.84 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.004 0.002 HIS A 264 PHE 0.013 0.001 PHE A 227 TYR 0.008 0.001 TYR B 98 ARG 0.002 0.000 ARG B 53 *********************** 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 54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 155 MET cc_start: 0.7700 (tpt) cc_final: 0.6577 (tmm) REVERT: A 308 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7625 (mtp180) REVERT: B 120 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: B 123 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.3900 (mtm-85) outliers start: 22 outliers final: 17 residues processed: 51 average time/residue: 0.1516 time to fit residues: 10.3634 Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 128 PHE 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 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 6 GLN 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: 0.6980 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 40.0000 chunk 13 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.065852 restraints weight = 12103.812| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.59 r_work: 0.2844 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.8021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4403 Z= 0.362 Angle : 0.611 5.699 6006 Z= 0.327 Chirality : 0.046 0.189 719 Planarity : 0.006 0.097 775 Dihedral : 4.800 41.194 630 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.02 % Favored : 92.29 % Rotamer: Outliers : 4.86 % Allowed : 22.92 % Favored : 72.22 % 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: -0.63 (0.36), residues: 584 helix: 2.07 (0.41), residues: 158 sheet: -0.47 (0.48), residues: 122 loop : -1.84 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.004 0.001 HIS A 264 PHE 0.014 0.001 PHE A 227 TYR 0.010 0.001 TYR B 139 ARG 0.002 0.000 ARG B 31 ********************** 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 56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: A 155 MET cc_start: 0.7862 (tpt) cc_final: 0.6663 (tmm) REVERT: A 308 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7577 (mtp180) REVERT: B 120 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: B 123 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.4943 (mtm-85) outliers start: 21 outliers final: 17 residues processed: 53 average time/residue: 0.1440 time to fit residues: 10.3101 Evaluate side-chains 56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 128 PHE 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 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 6 GLN 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 57 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.067078 restraints weight = 12097.349| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.60 r_work: 0.2871 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4403 Z= 0.245 Angle : 0.562 5.521 6006 Z= 0.301 Chirality : 0.044 0.184 719 Planarity : 0.005 0.097 775 Dihedral : 4.582 39.244 630 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.48 % Favored : 93.84 % Rotamer: Outliers : 4.86 % Allowed : 22.69 % Favored : 72.45 % 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: -0.56 (0.36), residues: 584 helix: 2.11 (0.41), residues: 159 sheet: -0.49 (0.50), residues: 112 loop : -1.73 (0.35), residues: 313 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 98 ARG 0.002 0.000 ARG A 258 =============================================================================== Job complete usr+sys time: 2824.01 seconds wall clock time: 51 minutes 47.87 seconds (3107.87 seconds total)