Starting phenix.real_space_refine on Mon Apr 28 03:46:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9l_39082/04_2025/8y9l_39082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9l_39082/04_2025/8y9l_39082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9l_39082/04_2025/8y9l_39082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9l_39082/04_2025/8y9l_39082.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9l_39082/04_2025/8y9l_39082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9l_39082/04_2025/8y9l_39082.cif" } resolution = 3.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.077 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 4299 2.51 5 N 1241 2.21 5 O 1401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7008 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6127 Classifications: {'peptide': 757} Link IDs: {'PTRANS': 26, 'TRANS': 730} Chain breaks: 5 Chain: "B" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 880 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 4, 'rna3p': 36} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.81 Number of scatterers: 7008 At special positions: 0 Unit cell: (86.355, 98.325, 101.745, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 41 15.00 Mg 1 11.99 O 1401 8.00 N 1241 7.00 C 4299 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: 2.28 Conformation dependent library (CDL) restraints added in 761.0 milliseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 47.0% alpha, 12.3% beta 8 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 3.667A pdb=" N TRP A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.976A pdb=" N ASP A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 53 " --> pdb=" O ARG A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 74 through 88 removed outlier: 3.588A pdb=" N ALA A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.801A pdb=" N SER A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.776A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 230 removed outlier: 3.594A pdb=" N HIS A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.913A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.687A pdb=" N LEU A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 314 removed outlier: 3.764A pdb=" N LYS A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.627A pdb=" N ILE A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 512 through 537 removed outlier: 3.925A pdb=" N SER A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.786A pdb=" N GLN A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 610 removed outlier: 3.773A pdb=" N LEU A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 649 removed outlier: 3.801A pdb=" N TYR A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.584A pdb=" N LEU A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 831 through 847 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 4.584A pdb=" N SER A 429 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU A 404 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 332 removed outlier: 4.919A pdb=" N PHE A 420 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 359 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A 17 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS A 357 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 349 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 342 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 489 removed outlier: 4.064A pdb=" N TYR A 494 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 460 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N PHE A 656 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY A 462 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N GLU A 658 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AA5, first strand: chain 'A' and resid 760 through 761 removed outlier: 3.569A pdb=" N GLU A 827 " --> pdb=" O HIS A 824 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 800 removed outlier: 3.747A pdb=" N ARG A 796 " --> pdb=" O THR A 808 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1042 1.27 - 1.41: 1928 1.41 - 1.54: 4114 1.54 - 1.68: 115 1.68 - 1.81: 39 Bond restraints: 7238 Sorted by residual: bond pdb=" C PRO A 7 " pdb=" O PRO A 7 " ideal model delta sigma weight residual 1.233 1.135 0.098 1.13e-02 7.83e+03 7.52e+01 bond pdb=" O3' C B 0 " pdb=" P A B 1 " ideal model delta sigma weight residual 1.607 1.515 0.092 1.50e-02 4.44e+03 3.78e+01 bond pdb=" O3' U B 2 " pdb=" P A B 3 " ideal model delta sigma weight residual 1.607 1.523 0.084 1.50e-02 4.44e+03 3.17e+01 bond pdb=" P U B 2 " pdb=" OP2 U B 2 " ideal model delta sigma weight residual 1.485 1.376 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" P U B 2 " pdb=" OP1 U B 2 " ideal model delta sigma weight residual 1.485 1.380 0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 7233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 9890 4.33 - 8.65: 50 8.65 - 12.98: 7 12.98 - 17.31: 3 17.31 - 21.64: 2 Bond angle restraints: 9952 Sorted by residual: angle pdb=" CA ILE A 6 " pdb=" C ILE A 6 " pdb=" O ILE A 6 " ideal model delta sigma weight residual 119.15 111.19 7.96 5.90e-01 2.87e+00 1.82e+02 angle pdb=" C PRO A 7 " pdb=" CA PRO A 7 " pdb=" CB PRO A 7 " ideal model delta sigma weight residual 111.46 97.82 13.64 1.21e+00 6.83e-01 1.27e+02 angle pdb=" O2' A B 3 " pdb=" C2' A B 3 " pdb=" C1' A B 3 " ideal model delta sigma weight residual 108.40 122.29 -13.89 1.50e+00 4.44e-01 8.57e+01 angle pdb=" CA ILE A 6 " pdb=" C ILE A 6 " pdb=" N PRO A 7 " ideal model delta sigma weight residual 119.22 125.85 -6.63 7.80e-01 1.64e+00 7.23e+01 angle pdb=" C4' A B 1 " pdb=" C3' A B 1 " pdb=" O3' A B 1 " ideal model delta sigma weight residual 109.40 122.07 -12.67 1.50e+00 4.44e-01 7.14e+01 ... (remaining 9947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.02: 4137 29.02 - 58.05: 232 58.05 - 87.07: 61 87.07 - 116.10: 2 116.10 - 145.12: 1 Dihedral angle restraints: 4433 sinusoidal: 2229 harmonic: 2204 Sorted by residual: dihedral pdb=" O4' U B -18 " pdb=" C1' U B -18 " pdb=" N1 U B -18 " pdb=" C2 U B -18 " ideal model delta sinusoidal sigma weight residual 200.00 54.88 145.12 1 1.50e+01 4.44e-03 7.77e+01 dihedral pdb=" O4' U B 5 " pdb=" C1' U B 5 " pdb=" N1 U B 5 " pdb=" C2 U B 5 " ideal model delta sinusoidal sigma weight residual -128.00 -23.43 -104.57 1 1.70e+01 3.46e-03 4.16e+01 dihedral pdb=" C3' U B 5 " pdb=" C4' U B 5 " pdb=" O4' U B 5 " pdb=" C1' U B 5 " ideal model delta sinusoidal sigma weight residual -2.00 40.96 -42.96 1 8.00e+00 1.56e-02 4.02e+01 ... (remaining 4430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 1099 0.208 - 0.417: 12 0.417 - 0.625: 2 0.625 - 0.833: 0 0.833 - 1.041: 1 Chirality restraints: 1114 Sorted by residual: chirality pdb=" C2' A B 3 " pdb=" C3' A B 3 " pdb=" O2' A B 3 " pdb=" C1' A B 3 " both_signs ideal model delta sigma weight residual False -2.75 -1.71 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" CA ILE A 6 " pdb=" N ILE A 6 " pdb=" C ILE A 6 " pdb=" CB ILE A 6 " both_signs ideal model delta sigma weight residual False 2.43 2.96 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -1.89 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 1111 not shown) Planarity restraints: 1115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 838 " -0.029 2.00e-02 2.50e+03 5.95e-02 3.54e+01 pdb=" C LYS A 838 " 0.103 2.00e-02 2.50e+03 pdb=" O LYS A 838 " -0.039 2.00e-02 2.50e+03 pdb=" N ASP A 839 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 852 " -0.430 9.50e-02 1.11e+02 1.93e-01 2.28e+01 pdb=" NE ARG A 852 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 852 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 852 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 852 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 853 " -0.330 9.50e-02 1.11e+02 1.48e-01 1.35e+01 pdb=" NE ARG A 853 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 853 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 853 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 853 " -0.013 2.00e-02 2.50e+03 ... (remaining 1112 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 48 2.54 - 3.13: 5128 3.13 - 3.72: 10538 3.72 - 4.31: 15108 4.31 - 4.90: 24814 Nonbonded interactions: 55636 Sorted by model distance: nonbonded pdb=" O2' C B 0 " pdb=" OP1 U B 2 " model vdw 1.953 3.040 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A 901 " model vdw 2.114 2.170 nonbonded pdb=" ND1 HIS A 4 " pdb=" O HIS A 430 " model vdw 2.175 3.120 nonbonded pdb=" OD2 ASP A 31 " pdb=" OH TYR A 195 " model vdw 2.185 3.040 nonbonded pdb=" ND2 ASN A 753 " pdb=" O PHE A 867 " model vdw 2.216 3.120 ... (remaining 55631 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: 1.260 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.006 0.109 7238 Z= 0.344 Angle : 0.903 21.637 9952 Z= 0.555 Chirality : 0.065 1.041 1114 Planarity : 0.009 0.193 1115 Dihedral : 17.888 145.122 3015 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % Rotamer: Outliers : 1.52 % Allowed : 0.91 % Favored : 97.57 % Cbeta Deviations : 0.42 % 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: -0.24 (0.30), residues: 745 helix: 0.37 (0.28), residues: 352 sheet: 0.03 (0.47), residues: 124 loop : -0.81 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 323 HIS 0.012 0.001 HIS A 4 PHE 0.026 0.002 PHE A 785 TYR 0.014 0.001 TYR A 214 ARG 0.006 0.001 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.19183 ( 315) hydrogen bonds : angle 7.30116 ( 880) covalent geometry : bond 0.00589 ( 7238) covalent geometry : angle 0.90284 ( 9952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.759 Fit side-chains REVERT: A 53 ASP cc_start: 0.7148 (m-30) cc_final: 0.6920 (t70) REVERT: A 186 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7819 (pttp) REVERT: A 295 TRP cc_start: 0.6543 (t60) cc_final: 0.6343 (t60) REVERT: A 399 ILE cc_start: 0.8192 (mp) cc_final: 0.7991 (mt) REVERT: A 491 ASP cc_start: 0.7077 (m-30) cc_final: 0.6812 (t0) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 1.0811 time to fit residues: 101.7042 Evaluate side-chains 63 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PRO Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 853 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 276 GLN A 603 ASN A 709 ASN A 753 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.194423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166596 restraints weight = 8229.746| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.65 r_work: 0.3728 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7238 Z= 0.124 Angle : 0.531 6.914 9952 Z= 0.277 Chirality : 0.040 0.352 1114 Planarity : 0.004 0.045 1115 Dihedral : 17.754 145.508 1500 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.37 % Allowed : 7.74 % Favored : 90.90 % 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: 0.37 (0.31), residues: 745 helix: 0.97 (0.28), residues: 353 sheet: 0.14 (0.49), residues: 118 loop : -0.53 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 323 HIS 0.004 0.001 HIS A 824 PHE 0.006 0.001 PHE A 531 TYR 0.011 0.001 TYR A 214 ARG 0.003 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 315) hydrogen bonds : angle 4.83401 ( 880) covalent geometry : bond 0.00266 ( 7238) covalent geometry : angle 0.53113 ( 9952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.682 Fit side-chains REVERT: A 17 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7866 (p90) REVERT: A 53 ASP cc_start: 0.7586 (m-30) cc_final: 0.6677 (t70) REVERT: A 186 LYS cc_start: 0.8299 (ptmm) cc_final: 0.8020 (pttp) REVERT: A 295 TRP cc_start: 0.6038 (t60) cc_final: 0.5790 (t60) REVERT: A 377 ARG cc_start: 0.7478 (ptt90) cc_final: 0.7028 (ptt-90) REVERT: A 491 ASP cc_start: 0.7513 (m-30) cc_final: 0.7017 (t0) outliers start: 9 outliers final: 2 residues processed: 72 average time/residue: 0.8316 time to fit residues: 64.8544 Evaluate side-chains 60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.7924 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.183751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154520 restraints weight = 8571.494| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.84 r_work: 0.3573 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7238 Z= 0.270 Angle : 0.665 7.519 9952 Z= 0.343 Chirality : 0.045 0.296 1114 Planarity : 0.005 0.047 1115 Dihedral : 17.906 145.570 1484 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.73 % Allowed : 9.10 % Favored : 88.16 % 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: -0.14 (0.30), residues: 745 helix: 0.47 (0.27), residues: 357 sheet: -0.23 (0.46), residues: 128 loop : -0.63 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 323 HIS 0.008 0.001 HIS A 824 PHE 0.012 0.002 PHE A 442 TYR 0.021 0.002 TYR A 214 ARG 0.004 0.001 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.06742 ( 315) hydrogen bonds : angle 4.97502 ( 880) covalent geometry : bond 0.00628 ( 7238) covalent geometry : angle 0.66512 ( 9952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.787 Fit side-chains REVERT: A 17 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7542 (p90) REVERT: A 186 LYS cc_start: 0.8519 (ptmm) cc_final: 0.8262 (pttp) REVERT: A 295 TRP cc_start: 0.6083 (t60) cc_final: 0.5880 (t60) REVERT: A 377 ARG cc_start: 0.7472 (ptt90) cc_final: 0.7007 (ptt-90) REVERT: A 391 ARG cc_start: 0.8558 (mmt180) cc_final: 0.8317 (tpm170) REVERT: A 795 VAL cc_start: 0.8411 (p) cc_final: 0.8202 (m) outliers start: 18 outliers final: 7 residues processed: 69 average time/residue: 1.4259 time to fit residues: 103.9183 Evaluate side-chains 65 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.187089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158244 restraints weight = 8543.938| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.94 r_work: 0.3608 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7238 Z= 0.117 Angle : 0.501 6.509 9952 Z= 0.260 Chirality : 0.039 0.287 1114 Planarity : 0.004 0.045 1115 Dihedral : 17.691 143.942 1484 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.06 % Allowed : 14.11 % Favored : 84.83 % 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: 0.40 (0.31), residues: 745 helix: 1.09 (0.28), residues: 353 sheet: -0.00 (0.48), residues: 119 loop : -0.60 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 323 HIS 0.006 0.001 HIS A 824 PHE 0.006 0.001 PHE A 339 TYR 0.011 0.001 TYR A 214 ARG 0.003 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 315) hydrogen bonds : angle 4.35185 ( 880) covalent geometry : bond 0.00255 ( 7238) covalent geometry : angle 0.50137 ( 9952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.777 Fit side-chains REVERT: A 17 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7557 (p90) REVERT: A 186 LYS cc_start: 0.8533 (ptmm) cc_final: 0.8309 (pttp) REVERT: A 232 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 357 LYS cc_start: 0.7279 (ptpp) cc_final: 0.6931 (ptpt) REVERT: A 377 ARG cc_start: 0.7381 (ptt90) cc_final: 0.6867 (ptt-90) REVERT: A 795 VAL cc_start: 0.8488 (p) cc_final: 0.8282 (m) outliers start: 7 outliers final: 1 residues processed: 68 average time/residue: 0.9220 time to fit residues: 67.5923 Evaluate side-chains 61 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 678 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.180184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150252 restraints weight = 8579.604| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.02 r_work: 0.3503 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7238 Z= 0.296 Angle : 0.702 14.794 9952 Z= 0.354 Chirality : 0.045 0.242 1114 Planarity : 0.005 0.046 1115 Dihedral : 17.935 143.532 1484 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.12 % Allowed : 14.11 % Favored : 83.76 % 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: -0.13 (0.30), residues: 745 helix: 0.58 (0.27), residues: 353 sheet: -0.23 (0.47), residues: 119 loop : -0.75 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 323 HIS 0.011 0.001 HIS A 824 PHE 0.013 0.002 PHE A 420 TYR 0.023 0.002 TYR A 648 ARG 0.004 0.001 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.06749 ( 315) hydrogen bonds : angle 4.78942 ( 880) covalent geometry : bond 0.00687 ( 7238) covalent geometry : angle 0.70243 ( 9952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.693 Fit side-chains REVERT: A 17 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7543 (p90) REVERT: A 186 LYS cc_start: 0.8564 (ptmm) cc_final: 0.8245 (pttp) REVERT: A 357 LYS cc_start: 0.7430 (ptpp) cc_final: 0.7129 (ptpt) REVERT: A 377 ARG cc_start: 0.7440 (ptt90) cc_final: 0.6909 (ptt-90) REVERT: A 391 ARG cc_start: 0.8538 (mmt180) cc_final: 0.8270 (tpm170) REVERT: A 725 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6870 (mp0) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 1.2237 time to fit residues: 93.5427 Evaluate side-chains 68 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 264 GLN A 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157099 restraints weight = 8460.165| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.96 r_work: 0.3599 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7238 Z= 0.113 Angle : 0.525 13.332 9952 Z= 0.264 Chirality : 0.039 0.215 1114 Planarity : 0.004 0.044 1115 Dihedral : 17.762 141.767 1484 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.37 % Allowed : 15.63 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.31), residues: 745 helix: 1.21 (0.28), residues: 352 sheet: -0.05 (0.47), residues: 119 loop : -0.60 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 323 HIS 0.006 0.001 HIS A 824 PHE 0.006 0.001 PHE A 728 TYR 0.018 0.001 TYR A 648 ARG 0.002 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 315) hydrogen bonds : angle 4.27424 ( 880) covalent geometry : bond 0.00244 ( 7238) covalent geometry : angle 0.52548 ( 9952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.504 Fit side-chains REVERT: A 17 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7521 (p90) REVERT: A 186 LYS cc_start: 0.8560 (ptmm) cc_final: 0.8336 (pttp) REVERT: A 357 LYS cc_start: 0.7364 (ptpp) cc_final: 0.7005 (ptpt) REVERT: A 377 ARG cc_start: 0.7428 (ptt90) cc_final: 0.7176 (ptt-90) REVERT: A 725 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6794 (mp0) REVERT: A 795 VAL cc_start: 0.8480 (p) cc_final: 0.8270 (m) outliers start: 9 outliers final: 2 residues processed: 75 average time/residue: 1.9370 time to fit residues: 155.9461 Evaluate side-chains 64 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151440 restraints weight = 8445.314| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.94 r_work: 0.3521 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7238 Z= 0.235 Angle : 0.641 13.267 9952 Z= 0.321 Chirality : 0.043 0.194 1114 Planarity : 0.005 0.046 1115 Dihedral : 17.924 141.448 1484 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.82 % Allowed : 16.24 % Favored : 81.94 % 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: 0.05 (0.30), residues: 745 helix: 0.79 (0.27), residues: 352 sheet: -0.17 (0.48), residues: 119 loop : -0.75 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 323 HIS 0.011 0.001 HIS A 824 PHE 0.010 0.002 PHE A 420 TYR 0.020 0.002 TYR A 214 ARG 0.003 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.06090 ( 315) hydrogen bonds : angle 4.62073 ( 880) covalent geometry : bond 0.00541 ( 7238) covalent geometry : angle 0.64068 ( 9952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.777 Fit side-chains REVERT: A 17 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7520 (p90) REVERT: A 186 LYS cc_start: 0.8562 (ptmm) cc_final: 0.8325 (pttp) REVERT: A 232 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 290 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5979 (mp) REVERT: A 357 LYS cc_start: 0.7438 (ptpp) cc_final: 0.7061 (ptpt) REVERT: A 377 ARG cc_start: 0.7440 (ptt90) cc_final: 0.6948 (ptt-90) REVERT: A 391 ARG cc_start: 0.8537 (mmt180) cc_final: 0.8261 (tpm170) REVERT: A 725 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6809 (mp0) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 1.4327 time to fit residues: 104.9348 Evaluate side-chains 71 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 76 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.182592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153193 restraints weight = 8493.233| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.95 r_work: 0.3554 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7238 Z= 0.153 Angle : 0.561 11.208 9952 Z= 0.283 Chirality : 0.040 0.229 1114 Planarity : 0.004 0.045 1115 Dihedral : 17.827 139.805 1484 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.06 % Allowed : 16.54 % Favored : 82.40 % 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: 0.21 (0.30), residues: 745 helix: 0.97 (0.28), residues: 352 sheet: -0.16 (0.48), residues: 119 loop : -0.69 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 323 HIS 0.009 0.001 HIS A 824 PHE 0.008 0.001 PHE A 867 TYR 0.014 0.001 TYR A 214 ARG 0.003 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 315) hydrogen bonds : angle 4.41154 ( 880) covalent geometry : bond 0.00345 ( 7238) covalent geometry : angle 0.56098 ( 9952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.722 Fit side-chains REVERT: A 17 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7475 (p90) REVERT: A 186 LYS cc_start: 0.8577 (ptmm) cc_final: 0.8339 (pttp) REVERT: A 357 LYS cc_start: 0.7388 (ptpp) cc_final: 0.7020 (ptpt) REVERT: A 377 ARG cc_start: 0.7435 (ptt90) cc_final: 0.6953 (ptt-90) REVERT: A 391 ARG cc_start: 0.8520 (mmt180) cc_final: 0.8293 (tpp-160) REVERT: A 725 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6779 (mp0) REVERT: A 795 VAL cc_start: 0.8471 (p) cc_final: 0.8253 (m) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 1.1961 time to fit residues: 88.9252 Evaluate side-chains 69 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151286 restraints weight = 8639.250| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.96 r_work: 0.3518 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7238 Z= 0.229 Angle : 0.633 10.254 9952 Z= 0.320 Chirality : 0.043 0.198 1114 Planarity : 0.005 0.045 1115 Dihedral : 17.944 139.006 1484 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.52 % Allowed : 16.54 % Favored : 81.94 % 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: -0.08 (0.30), residues: 745 helix: 0.70 (0.28), residues: 352 sheet: -0.25 (0.48), residues: 119 loop : -0.82 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.004 TRP A 323 HIS 0.008 0.001 HIS A 824 PHE 0.011 0.002 PHE A 420 TYR 0.019 0.002 TYR A 214 ARG 0.003 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.06082 ( 315) hydrogen bonds : angle 4.62220 ( 880) covalent geometry : bond 0.00528 ( 7238) covalent geometry : angle 0.63257 ( 9952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.697 Fit side-chains REVERT: A 17 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7486 (p90) REVERT: A 186 LYS cc_start: 0.8570 (ptmm) cc_final: 0.8323 (pttp) REVERT: A 357 LYS cc_start: 0.7394 (ptpp) cc_final: 0.7104 (ptpt) REVERT: A 377 ARG cc_start: 0.7456 (ptt90) cc_final: 0.6963 (ptt-90) REVERT: A 391 ARG cc_start: 0.8559 (mmt180) cc_final: 0.8281 (tpm170) REVERT: A 446 LYS cc_start: 0.7952 (mmpt) cc_final: 0.7664 (mmpt) REVERT: A 725 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6829 (mp0) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 1.4691 time to fit residues: 106.9024 Evaluate side-chains 70 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.184997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155709 restraints weight = 8657.026| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.96 r_work: 0.3574 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7238 Z= 0.128 Angle : 0.537 8.560 9952 Z= 0.273 Chirality : 0.039 0.192 1114 Planarity : 0.004 0.044 1115 Dihedral : 17.799 137.661 1484 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.76 % Allowed : 17.15 % Favored : 82.09 % 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: 0.30 (0.30), residues: 745 helix: 1.06 (0.28), residues: 352 sheet: -0.14 (0.48), residues: 119 loop : -0.66 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP A 323 HIS 0.007 0.001 HIS A 824 PHE 0.007 0.001 PHE A 867 TYR 0.013 0.001 TYR A 648 ARG 0.003 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 315) hydrogen bonds : angle 4.32490 ( 880) covalent geometry : bond 0.00283 ( 7238) covalent geometry : angle 0.53670 ( 9952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.913 Fit side-chains REVERT: A 17 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7479 (p90) REVERT: A 186 LYS cc_start: 0.8601 (ptmm) cc_final: 0.8359 (pttp) REVERT: A 357 LYS cc_start: 0.7388 (ptpp) cc_final: 0.7026 (ptpt) REVERT: A 377 ARG cc_start: 0.7418 (ptt90) cc_final: 0.6931 (ptt-90) REVERT: A 391 ARG cc_start: 0.8557 (mmt180) cc_final: 0.8327 (tpp-160) REVERT: A 446 LYS cc_start: 0.7892 (mmpt) cc_final: 0.7333 (mptm) REVERT: A 725 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6793 (mp0) REVERT: A 795 VAL cc_start: 0.8460 (p) cc_final: 0.8224 (m) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 1.6994 time to fit residues: 130.1122 Evaluate side-chains 69 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 824 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.184507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155123 restraints weight = 8544.567| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.94 r_work: 0.3568 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7238 Z= 0.138 Angle : 0.538 8.008 9952 Z= 0.273 Chirality : 0.039 0.182 1114 Planarity : 0.004 0.044 1115 Dihedral : 17.741 137.030 1484 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.61 % Allowed : 17.75 % Favored : 81.64 % 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: 0.40 (0.30), residues: 745 helix: 1.15 (0.28), residues: 352 sheet: -0.08 (0.49), residues: 119 loop : -0.64 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP A 323 HIS 0.009 0.001 HIS A 824 PHE 0.007 0.001 PHE A 35 TYR 0.013 0.001 TYR A 648 ARG 0.003 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 315) hydrogen bonds : angle 4.28000 ( 880) covalent geometry : bond 0.00309 ( 7238) covalent geometry : angle 0.53798 ( 9952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5664.64 seconds wall clock time: 102 minutes 16.35 seconds (6136.35 seconds total)