Starting phenix.real_space_refine on Sat May 10 05:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co9_45774/05_2025/9co9_45774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co9_45774/05_2025/9co9_45774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9co9_45774/05_2025/9co9_45774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co9_45774/05_2025/9co9_45774.map" model { file = "/net/cci-nas-00/data/ceres_data/9co9_45774/05_2025/9co9_45774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co9_45774/05_2025/9co9_45774.cif" } resolution = 3.44 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= 0.007 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 26 5.16 5 C 3305 2.51 5 N 882 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5198 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1608 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 14, 'TRANS': 185} Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1634 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 14, 'TRANS': 188} Chain: "D" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Time building chain proxies: 5.39, per 1000 atoms: 1.04 Number of scatterers: 5198 At special positions: 0 Unit cell: (82.336, 109.781, 118.635, 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 26 16.00 O 985 8.00 N 882 7.00 C 3305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.05 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.05 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 104 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 50 " - pdb=" SG CYS E 104 " distance=2.03 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: 1.20 Conformation dependent library (CDL) restraints added in 537.6 milliseconds 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 10.4% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.765A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 3.759A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.551A pdb=" N GLN B 502 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.879A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.587A pdb=" N VAL A 404 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.600A pdb=" N ASP D 90 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR D 91 " --> pdb=" O LEU D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.986A pdb=" N THR E 91 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.979A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 428 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR B 377 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AA3, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.514A pdb=" N TYR B 470 " --> pdb=" O TYR B 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.537A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 355 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN A 391 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLU A 512 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.504A pdb=" N VAL D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.167A pdb=" N GLY D 10 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 12 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR D 34 " --> pdb=" O CYS D 50 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS D 50 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.633A pdb=" N GLY E 10 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N CYS E 50 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 315 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: 1.04 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1668 1.35 - 1.47: 1458 1.47 - 1.60: 2192 1.60 - 1.73: 0 1.73 - 1.85: 28 Bond restraints: 5346 Sorted by residual: bond pdb=" C PHE B 326 " pdb=" N PRO B 327 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.28e-02 6.10e+03 1.12e+01 bond pdb=" N GLY A 473 " pdb=" CA GLY A 473 " ideal model delta sigma weight residual 1.445 1.475 -0.031 9.90e-03 1.02e+04 9.66e+00 bond pdb=" N TYR D 110 " pdb=" CA TYR D 110 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.36e-02 5.41e+03 8.63e+00 bond pdb=" N GLN A 489 " pdb=" CA GLN A 489 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.43e+00 bond pdb=" N HIS D 32 " pdb=" CA HIS D 32 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.18e-02 7.18e+03 8.15e+00 ... (remaining 5341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 6948 2.33 - 4.66: 259 4.66 - 6.99: 42 6.99 - 9.32: 12 9.32 - 11.65: 2 Bond angle restraints: 7263 Sorted by residual: angle pdb=" N HIS D 30 " pdb=" CA HIS D 30 " pdb=" C HIS D 30 " ideal model delta sigma weight residual 114.64 102.99 11.65 1.52e+00 4.33e-01 5.88e+01 angle pdb=" CA PHE A 339 " pdb=" CB PHE A 339 " pdb=" CG PHE A 339 " ideal model delta sigma weight residual 113.80 120.08 -6.28 1.00e+00 1.00e+00 3.95e+01 angle pdb=" CA TYR D 110 " pdb=" CB TYR D 110 " pdb=" CG TYR D 110 " ideal model delta sigma weight residual 113.90 123.49 -9.59 1.80e+00 3.09e-01 2.84e+01 angle pdb=" N THR D 31 " pdb=" CA THR D 31 " pdb=" C THR D 31 " ideal model delta sigma weight residual 114.12 107.44 6.68 1.39e+00 5.18e-01 2.31e+01 angle pdb=" O TYR D 109 " pdb=" C TYR D 109 " pdb=" N TYR D 110 " ideal model delta sigma weight residual 123.27 117.86 5.41 1.16e+00 7.43e-01 2.18e+01 ... (remaining 7258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2839 17.97 - 35.93: 251 35.93 - 53.90: 35 53.90 - 71.86: 8 71.86 - 89.82: 2 Dihedral angle restraints: 3135 sinusoidal: 1222 harmonic: 1913 Sorted by residual: dihedral pdb=" CB CYS B 477 " pdb=" SG CYS B 477 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -16.00 -70.00 1 1.00e+01 1.00e-02 6.32e+01 dihedral pdb=" CB CYS A 388 " pdb=" SG CYS A 388 " pdb=" SG CYS A 521 " pdb=" CB CYS A 521 " ideal model delta sinusoidal sigma weight residual 93.00 38.69 54.31 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 140.44 -47.44 1 1.00e+01 1.00e-02 3.11e+01 ... (remaining 3132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 502 0.053 - 0.106: 188 0.106 - 0.159: 49 0.159 - 0.213: 12 0.213 - 0.266: 2 Chirality restraints: 753 Sorted by residual: chirality pdb=" CA PRO A 495 " pdb=" N PRO A 495 " pdb=" C PRO A 495 " pdb=" CB PRO A 495 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE A 465 " pdb=" N ILE A 465 " pdb=" C ILE A 465 " pdb=" CB ILE A 465 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASN A 391 " pdb=" N ASN A 391 " pdb=" C ASN A 391 " pdb=" CB ASN A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 750 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 109 " 0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C TYR D 109 " -0.070 2.00e-02 2.50e+03 pdb=" O TYR D 109 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR D 110 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 494 " -0.315 9.50e-02 1.11e+02 1.41e-01 1.22e+01 pdb=" NE ARG A 494 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 494 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 494 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 494 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 28 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C ALA D 28 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA D 28 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU D 29 " 0.015 2.00e-02 2.50e+03 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1747 2.84 - 3.36: 4242 3.36 - 3.87: 8070 3.87 - 4.39: 9034 4.39 - 4.90: 15888 Nonbonded interactions: 38981 Sorted by model distance: nonbonded pdb=" O ASP D 114 " pdb=" N PHE D 116 " model vdw 2.330 3.120 nonbonded pdb=" O LEU D 29 " pdb=" NH1 ARG D 72 " model vdw 2.348 3.120 nonbonded pdb=" OG1 THR B 412 " pdb=" OD2 ASP B 417 " model vdw 2.350 3.040 nonbonded pdb=" O SER B 510 " pdb=" OG SER B 510 " model vdw 2.387 3.040 nonbonded pdb=" OD2 ASP A 395 " pdb=" OH TYR A 420 " model vdw 2.405 3.040 ... (remaining 38976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 326 through 525) selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 6.900 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.150 Process input model: 18.540 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 0.049 5358 Z= 0.357 Angle : 1.025 11.654 7287 Z= 0.611 Chirality : 0.059 0.266 753 Planarity : 0.008 0.141 950 Dihedral : 12.974 89.824 1893 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.28 % Favored : 93.11 % Rotamer: Outliers : 0.72 % Allowed : 1.43 % Favored : 97.85 % 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: -2.36 (0.30), residues: 653 helix: -4.28 (0.37), residues: 51 sheet: 0.13 (0.45), residues: 147 loop : -1.96 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 449 HIS 0.007 0.001 HIS A 336 PHE 0.032 0.002 PHE A 335 TYR 0.031 0.002 TYR D 110 ARG 0.014 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.27164 ( 131) hydrogen bonds : angle 9.56907 ( 315) SS BOND : bond 0.00906 ( 12) SS BOND : angle 1.80048 ( 24) covalent geometry : bond 0.00568 ( 5346) covalent geometry : angle 1.02104 ( 7263) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 209 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 TYR cc_start: 0.7805 (m-80) cc_final: 0.6855 (m-80) outliers start: 4 outliers final: 1 residues processed: 211 average time/residue: 0.2423 time to fit residues: 62.3015 Evaluate side-chains 132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN D 82 GLN D 121 GLN E 13 GLN E 32 HIS E 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083647 restraints weight = 13780.818| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.32 r_work: 0.3172 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5358 Z= 0.158 Angle : 0.754 9.141 7287 Z= 0.385 Chirality : 0.048 0.173 753 Planarity : 0.005 0.048 950 Dihedral : 5.386 26.271 738 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.49 % Rotamer: Outliers : 1.79 % Allowed : 16.10 % Favored : 82.11 % 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: -1.87 (0.31), residues: 653 helix: -3.80 (0.46), residues: 55 sheet: 0.41 (0.42), residues: 171 loop : -1.69 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 449 HIS 0.004 0.001 HIS B 515 PHE 0.021 0.001 PHE E 68 TYR 0.024 0.002 TYR D 110 ARG 0.009 0.001 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 131) hydrogen bonds : angle 6.83655 ( 315) SS BOND : bond 0.00676 ( 12) SS BOND : angle 2.30679 ( 24) covalent geometry : bond 0.00367 ( 5346) covalent geometry : angle 0.74341 ( 7263) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8412 (tpp80) REVERT: B 411 GLN cc_start: 0.7385 (mp10) cc_final: 0.7109 (mp10) REVERT: B 462 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 403 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8730 (mt-10) REVERT: A 464 ASP cc_start: 0.8435 (t0) cc_final: 0.8144 (t0) REVERT: A 496 THR cc_start: 0.8853 (p) cc_final: 0.8567 (p) REVERT: A 514 LEU cc_start: 0.7158 (tt) cc_final: 0.6533 (tt) REVERT: D 36 TRP cc_start: 0.8085 (m100) cc_final: 0.7827 (m100) REVERT: D 44 GLU cc_start: 0.8243 (tp30) cc_final: 0.7545 (tp30) REVERT: D 59 TYR cc_start: 0.8889 (m-80) cc_final: 0.8216 (m-80) REVERT: D 77 ASN cc_start: 0.8841 (t0) cc_final: 0.7857 (t0) REVERT: D 95 TYR cc_start: 0.7321 (m-80) cc_final: 0.7106 (m-80) REVERT: D 115 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8001 (p0) REVERT: D 125 VAL cc_start: 0.9247 (t) cc_final: 0.9017 (p) REVERT: E 13 GLN cc_start: 0.8417 (mm110) cc_final: 0.8175 (mm-40) REVERT: E 19 ARG cc_start: 0.9054 (ttt-90) cc_final: 0.8688 (ttt-90) REVERT: E 87 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8227 (ttpt) REVERT: E 89 GLU cc_start: 0.9188 (pm20) cc_final: 0.7875 (pm20) outliers start: 10 outliers final: 7 residues processed: 150 average time/residue: 0.1783 time to fit residues: 33.8568 Evaluate side-chains 133 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.108630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082769 restraints weight = 14083.974| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.37 r_work: 0.3138 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5358 Z= 0.155 Angle : 0.693 8.626 7287 Z= 0.354 Chirality : 0.046 0.166 753 Planarity : 0.005 0.047 950 Dihedral : 5.080 22.916 736 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.13 % Favored : 93.57 % Rotamer: Outliers : 2.86 % Allowed : 17.89 % Favored : 79.25 % 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: -1.79 (0.31), residues: 653 helix: -3.52 (0.54), residues: 47 sheet: 0.44 (0.40), residues: 182 loop : -1.76 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 PHE 0.026 0.001 PHE E 68 TYR 0.033 0.001 TYR D 94 ARG 0.005 0.001 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 131) hydrogen bonds : angle 6.61845 ( 315) SS BOND : bond 0.00499 ( 12) SS BOND : angle 1.96311 ( 24) covalent geometry : bond 0.00364 ( 5346) covalent geometry : angle 0.68464 ( 7263) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 343 ARG cc_start: 0.8833 (ptp90) cc_final: 0.8594 (ptp90) REVERT: B 395 ASP cc_start: 0.9031 (p0) cc_final: 0.8652 (p0) REVERT: A 403 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8795 (mt-10) REVERT: A 464 ASP cc_start: 0.8400 (t0) cc_final: 0.8170 (t0) REVERT: D 19 ARG cc_start: 0.9211 (ttm-80) cc_final: 0.8940 (ttt90) REVERT: D 44 GLU cc_start: 0.8351 (tp30) cc_final: 0.7791 (tp30) REVERT: D 59 TYR cc_start: 0.8882 (m-80) cc_final: 0.8305 (m-80) REVERT: D 77 ASN cc_start: 0.8674 (t0) cc_final: 0.7753 (t0) REVERT: D 109 TYR cc_start: 0.8688 (t80) cc_final: 0.8453 (t80) REVERT: D 113 ASP cc_start: 0.8532 (m-30) cc_final: 0.7887 (t0) REVERT: E 3 GLN cc_start: 0.8785 (mm110) cc_final: 0.7528 (mm-40) outliers start: 16 outliers final: 11 residues processed: 140 average time/residue: 0.1882 time to fit residues: 34.3986 Evaluate side-chains 131 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.108909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.083279 restraints weight = 14070.279| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.33 r_work: 0.3145 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5358 Z= 0.141 Angle : 0.694 8.625 7287 Z= 0.353 Chirality : 0.045 0.171 753 Planarity : 0.004 0.038 950 Dihedral : 5.182 30.601 736 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.90 % Favored : 94.79 % Rotamer: Outliers : 3.94 % Allowed : 18.07 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.65 (0.32), residues: 653 helix: -3.38 (0.57), residues: 48 sheet: 0.34 (0.38), residues: 195 loop : -1.62 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 PHE 0.014 0.001 PHE E 68 TYR 0.039 0.001 TYR D 94 ARG 0.004 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 131) hydrogen bonds : angle 6.40722 ( 315) SS BOND : bond 0.00475 ( 12) SS BOND : angle 1.56240 ( 24) covalent geometry : bond 0.00329 ( 5346) covalent geometry : angle 0.68981 ( 7263) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 ASP cc_start: 0.9049 (p0) cc_final: 0.8401 (p0) REVERT: A 403 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8843 (mt-10) REVERT: A 464 ASP cc_start: 0.8430 (t0) cc_final: 0.8108 (t0) REVERT: D 19 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8872 (ttt90) REVERT: D 44 GLU cc_start: 0.8331 (tp30) cc_final: 0.7944 (tp30) REVERT: D 59 TYR cc_start: 0.8892 (m-80) cc_final: 0.8344 (m-80) REVERT: D 77 ASN cc_start: 0.8803 (t0) cc_final: 0.7909 (t0) REVERT: D 109 TYR cc_start: 0.8655 (t80) cc_final: 0.8428 (t80) REVERT: D 113 ASP cc_start: 0.8486 (m-30) cc_final: 0.7743 (t0) REVERT: D 117 TYR cc_start: 0.8536 (t80) cc_final: 0.7602 (t80) REVERT: E 3 GLN cc_start: 0.8650 (mm110) cc_final: 0.8306 (mm110) outliers start: 22 outliers final: 12 residues processed: 137 average time/residue: 0.1546 time to fit residues: 27.8321 Evaluate side-chains 135 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.107113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082606 restraints weight = 14078.795| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 4.36 r_work: 0.3110 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5358 Z= 0.163 Angle : 0.698 8.862 7287 Z= 0.356 Chirality : 0.046 0.164 753 Planarity : 0.004 0.038 950 Dihedral : 4.964 21.250 736 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.82 % Favored : 93.87 % Rotamer: Outliers : 3.22 % Allowed : 19.68 % Favored : 77.10 % 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: -1.55 (0.32), residues: 653 helix: -3.37 (0.58), residues: 48 sheet: 0.44 (0.39), residues: 195 loop : -1.54 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.004 0.001 HIS B 515 PHE 0.012 0.001 PHE D 37 TYR 0.017 0.001 TYR D 94 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 131) hydrogen bonds : angle 6.22324 ( 315) SS BOND : bond 0.00493 ( 12) SS BOND : angle 1.29841 ( 24) covalent geometry : bond 0.00381 ( 5346) covalent geometry : angle 0.69485 ( 7263) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8173 (t80) cc_final: 0.7741 (t80) REVERT: B 395 ASP cc_start: 0.8963 (p0) cc_final: 0.8580 (p0) REVERT: B 512 GLU cc_start: 0.8938 (pt0) cc_final: 0.8404 (pp20) REVERT: A 389 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8536 (p90) REVERT: A 403 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8861 (mt-10) REVERT: A 464 ASP cc_start: 0.8358 (t0) cc_final: 0.8002 (t0) REVERT: D 19 ARG cc_start: 0.9261 (ttm-80) cc_final: 0.9036 (ttt90) REVERT: D 44 GLU cc_start: 0.8481 (tp30) cc_final: 0.8110 (tp30) REVERT: D 59 TYR cc_start: 0.8905 (m-80) cc_final: 0.8413 (m-80) REVERT: D 77 ASN cc_start: 0.8922 (t0) cc_final: 0.8052 (t0) REVERT: D 109 TYR cc_start: 0.8663 (t80) cc_final: 0.8277 (t80) REVERT: D 113 ASP cc_start: 0.8433 (m-30) cc_final: 0.7602 (t0) REVERT: D 117 TYR cc_start: 0.8649 (t80) cc_final: 0.7686 (t80) REVERT: E 44 GLU cc_start: 0.8857 (mp0) cc_final: 0.8232 (mp0) REVERT: E 46 GLU cc_start: 0.7889 (pm20) cc_final: 0.7395 (pm20) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.1655 time to fit residues: 28.4435 Evaluate side-chains 132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.0470 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.107484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.082601 restraints weight = 13836.471| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.42 r_work: 0.3118 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5358 Z= 0.142 Angle : 0.685 8.561 7287 Z= 0.350 Chirality : 0.045 0.161 753 Planarity : 0.004 0.039 950 Dihedral : 4.827 20.182 736 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.90 % Favored : 94.79 % Rotamer: Outliers : 3.76 % Allowed : 20.75 % Favored : 75.49 % 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: -1.48 (0.32), residues: 653 helix: -3.40 (0.52), residues: 55 sheet: 0.49 (0.39), residues: 193 loop : -1.43 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS B 515 PHE 0.009 0.001 PHE D 37 TYR 0.012 0.001 TYR D 111 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 131) hydrogen bonds : angle 6.10347 ( 315) SS BOND : bond 0.00515 ( 12) SS BOND : angle 1.17261 ( 24) covalent geometry : bond 0.00333 ( 5346) covalent geometry : angle 0.68316 ( 7263) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8170 (t80) cc_final: 0.7726 (t80) REVERT: B 395 ASP cc_start: 0.8940 (p0) cc_final: 0.8444 (p0) REVERT: B 512 GLU cc_start: 0.9008 (pt0) cc_final: 0.8485 (pp20) REVERT: A 403 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8865 (mt-10) REVERT: A 464 ASP cc_start: 0.8382 (t0) cc_final: 0.8043 (t0) REVERT: D 44 GLU cc_start: 0.8466 (tp30) cc_final: 0.8237 (tp30) REVERT: D 46 GLU cc_start: 0.7815 (pm20) cc_final: 0.7607 (pm20) REVERT: D 59 TYR cc_start: 0.9036 (m-80) cc_final: 0.8476 (m-80) REVERT: D 77 ASN cc_start: 0.8972 (t0) cc_final: 0.8165 (t0) REVERT: D 82 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8530 (tm-30) REVERT: D 109 TYR cc_start: 0.8672 (t80) cc_final: 0.8379 (t80) REVERT: D 113 ASP cc_start: 0.8413 (m-30) cc_final: 0.7289 (t0) REVERT: D 115 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7504 (p0) REVERT: D 117 TYR cc_start: 0.8712 (t80) cc_final: 0.7715 (t80) REVERT: E 44 GLU cc_start: 0.8857 (mp0) cc_final: 0.8281 (mp0) REVERT: E 46 GLU cc_start: 0.7969 (pm20) cc_final: 0.7468 (pm20) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.1605 time to fit residues: 28.4632 Evaluate side-chains 130 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 0.1980 chunk 8 optimal weight: 0.0670 chunk 44 optimal weight: 0.0040 chunk 58 optimal weight: 0.0020 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN E 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083336 restraints weight = 13902.113| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.38 r_work: 0.3161 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5358 Z= 0.118 Angle : 0.682 8.345 7287 Z= 0.348 Chirality : 0.045 0.166 753 Planarity : 0.004 0.041 950 Dihedral : 4.573 17.962 736 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.44 % Favored : 95.25 % Rotamer: Outliers : 3.22 % Allowed : 21.82 % Favored : 74.96 % 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: -1.39 (0.32), residues: 653 helix: -3.30 (0.53), residues: 55 sheet: 0.76 (0.41), residues: 171 loop : -1.38 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.004 0.001 HIS D 32 PHE 0.011 0.001 PHE D 37 TYR 0.011 0.001 TYR E 59 ARG 0.006 0.000 ARG B 343 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 131) hydrogen bonds : angle 6.02842 ( 315) SS BOND : bond 0.00434 ( 12) SS BOND : angle 1.07605 ( 24) covalent geometry : bond 0.00277 ( 5346) covalent geometry : angle 0.68066 ( 7263) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8177 (t80) cc_final: 0.7745 (t80) REVERT: B 395 ASP cc_start: 0.8907 (p0) cc_final: 0.8401 (p0) REVERT: B 462 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7531 (tm-30) REVERT: B 512 GLU cc_start: 0.9058 (pt0) cc_final: 0.8453 (pp20) REVERT: B 514 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (mm) REVERT: A 403 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8844 (mt-10) REVERT: A 464 ASP cc_start: 0.8383 (t0) cc_final: 0.8037 (t0) REVERT: A 496 THR cc_start: 0.8932 (p) cc_final: 0.8682 (p) REVERT: D 44 GLU cc_start: 0.8754 (tp30) cc_final: 0.8261 (tp30) REVERT: D 59 TYR cc_start: 0.9061 (m-80) cc_final: 0.8344 (m-80) REVERT: D 67 ARG cc_start: 0.9093 (mtm-85) cc_final: 0.8873 (mtm-85) REVERT: D 77 ASN cc_start: 0.8951 (t0) cc_final: 0.8299 (t0) REVERT: D 82 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8554 (tm-30) REVERT: D 113 ASP cc_start: 0.8389 (m-30) cc_final: 0.7369 (t0) REVERT: D 115 ASP cc_start: 0.8378 (m-30) cc_final: 0.7536 (p0) REVERT: D 117 TYR cc_start: 0.8657 (t80) cc_final: 0.7741 (t80) REVERT: D 121 GLN cc_start: 0.8799 (mp10) cc_final: 0.8574 (mp10) REVERT: E 3 GLN cc_start: 0.8825 (mm110) cc_final: 0.8540 (mm-40) REVERT: E 44 GLU cc_start: 0.8823 (mp0) cc_final: 0.8250 (mp0) REVERT: E 46 GLU cc_start: 0.7873 (pm20) cc_final: 0.7400 (pm20) outliers start: 18 outliers final: 16 residues processed: 137 average time/residue: 0.1740 time to fit residues: 31.5883 Evaluate side-chains 141 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 76 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.107405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082542 restraints weight = 13991.499| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.34 r_work: 0.3117 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5358 Z= 0.154 Angle : 0.699 8.299 7287 Z= 0.359 Chirality : 0.045 0.168 753 Planarity : 0.004 0.041 950 Dihedral : 4.725 21.372 736 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.36 % Favored : 94.33 % Rotamer: Outliers : 3.58 % Allowed : 21.65 % Favored : 74.78 % 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: -1.44 (0.32), residues: 653 helix: -3.24 (0.55), residues: 55 sheet: 0.54 (0.40), residues: 185 loop : -1.41 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS B 515 PHE 0.027 0.001 PHE E 68 TYR 0.010 0.001 TYR B 377 ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 131) hydrogen bonds : angle 5.99301 ( 315) SS BOND : bond 0.00460 ( 12) SS BOND : angle 1.14844 ( 24) covalent geometry : bond 0.00364 ( 5346) covalent geometry : angle 0.69655 ( 7263) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8253 (t80) cc_final: 0.7650 (t80) REVERT: B 390 THR cc_start: 0.9397 (p) cc_final: 0.9092 (p) REVERT: B 395 ASP cc_start: 0.8968 (p0) cc_final: 0.8477 (p0) REVERT: B 462 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7628 (tm-30) REVERT: B 512 GLU cc_start: 0.9095 (pt0) cc_final: 0.8562 (pp20) REVERT: B 514 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 403 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8870 (mt-10) REVERT: A 464 ASP cc_start: 0.8360 (t0) cc_final: 0.7989 (t70) REVERT: D 3 GLN cc_start: 0.8485 (pm20) cc_final: 0.8227 (pm20) REVERT: D 44 GLU cc_start: 0.8704 (tp30) cc_final: 0.8339 (tp30) REVERT: D 59 TYR cc_start: 0.9080 (m-80) cc_final: 0.8553 (m-80) REVERT: D 67 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8648 (mtm110) REVERT: D 77 ASN cc_start: 0.9114 (t0) cc_final: 0.8453 (t0) REVERT: D 80 TYR cc_start: 0.8500 (m-80) cc_final: 0.8168 (m-80) REVERT: D 82 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8447 (tm-30) REVERT: D 83 MET cc_start: 0.8668 (mmm) cc_final: 0.8349 (mmm) REVERT: D 117 TYR cc_start: 0.8775 (t80) cc_final: 0.7784 (t80) REVERT: D 121 GLN cc_start: 0.8762 (mp10) cc_final: 0.8294 (pm20) REVERT: E 44 GLU cc_start: 0.8889 (mp0) cc_final: 0.8339 (mp0) REVERT: E 46 GLU cc_start: 0.8043 (pm20) cc_final: 0.7571 (pm20) outliers start: 20 outliers final: 15 residues processed: 130 average time/residue: 0.1729 time to fit residues: 28.9928 Evaluate side-chains 128 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 113 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.107178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082004 restraints weight = 13903.535| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.43 r_work: 0.3110 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5358 Z= 0.161 Angle : 0.724 8.577 7287 Z= 0.370 Chirality : 0.046 0.169 753 Planarity : 0.004 0.041 950 Dihedral : 4.917 30.009 736 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.05 % Favored : 94.64 % Rotamer: Outliers : 3.76 % Allowed : 21.29 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.50 (0.32), residues: 653 helix: -3.22 (0.54), residues: 55 sheet: 0.53 (0.40), residues: 185 loop : -1.48 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS B 515 PHE 0.025 0.001 PHE E 68 TYR 0.010 0.001 TYR B 491 ARG 0.005 0.000 ARG B 343 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 131) hydrogen bonds : angle 6.00064 ( 315) SS BOND : bond 0.00458 ( 12) SS BOND : angle 1.54037 ( 24) covalent geometry : bond 0.00380 ( 5346) covalent geometry : angle 0.71994 ( 7263) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8304 (t80) cc_final: 0.7685 (t80) REVERT: B 390 THR cc_start: 0.9401 (p) cc_final: 0.8907 (p) REVERT: B 395 ASP cc_start: 0.8970 (p0) cc_final: 0.8484 (p0) REVERT: B 462 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 514 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8040 (mm) REVERT: A 403 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8892 (mt-10) REVERT: A 464 ASP cc_start: 0.8360 (t0) cc_final: 0.7987 (t70) REVERT: D 3 GLN cc_start: 0.8416 (pm20) cc_final: 0.8196 (pm20) REVERT: D 44 GLU cc_start: 0.8743 (tp30) cc_final: 0.8378 (tp30) REVERT: D 59 TYR cc_start: 0.9126 (m-80) cc_final: 0.8554 (m-80) REVERT: D 67 ARG cc_start: 0.9101 (mtm-85) cc_final: 0.8792 (mtm-85) REVERT: D 76 LYS cc_start: 0.9606 (ptpp) cc_final: 0.9302 (ptpp) REVERT: D 77 ASN cc_start: 0.9132 (t0) cc_final: 0.8579 (t0) REVERT: D 80 TYR cc_start: 0.8503 (m-80) cc_final: 0.8096 (m-80) REVERT: D 82 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8518 (tm-30) REVERT: D 83 MET cc_start: 0.8677 (mmm) cc_final: 0.8349 (mmm) REVERT: D 121 GLN cc_start: 0.8751 (mp10) cc_final: 0.8294 (pm20) REVERT: E 44 GLU cc_start: 0.8935 (mp0) cc_final: 0.8316 (mp0) REVERT: E 46 GLU cc_start: 0.8144 (pm20) cc_final: 0.7617 (pm20) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 0.1552 time to fit residues: 26.7740 Evaluate side-chains 131 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 113 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 chunk 50 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082976 restraints weight = 13981.283| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.44 r_work: 0.3129 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5358 Z= 0.135 Angle : 0.708 8.253 7287 Z= 0.363 Chirality : 0.046 0.167 753 Planarity : 0.004 0.041 950 Dihedral : 4.657 17.800 736 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.90 % Favored : 94.79 % Rotamer: Outliers : 2.86 % Allowed : 22.90 % Favored : 74.24 % 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: -1.45 (0.32), residues: 653 helix: -3.08 (0.55), residues: 55 sheet: 0.50 (0.40), residues: 185 loop : -1.42 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.004 0.001 HIS B 515 PHE 0.009 0.001 PHE E 68 TYR 0.009 0.001 TYR D 111 ARG 0.006 0.000 ARG B 343 Details of bonding type rmsd hydrogen bonds : bond 0.02987 ( 131) hydrogen bonds : angle 5.95788 ( 315) SS BOND : bond 0.00467 ( 12) SS BOND : angle 1.11792 ( 24) covalent geometry : bond 0.00318 ( 5346) covalent geometry : angle 0.70616 ( 7263) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1306 Ramachandran restraints generated. 653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8228 (t80) cc_final: 0.7601 (t80) REVERT: B 390 THR cc_start: 0.9352 (p) cc_final: 0.9066 (p) REVERT: B 395 ASP cc_start: 0.8987 (p0) cc_final: 0.8524 (p0) REVERT: B 462 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 512 GLU cc_start: 0.8949 (pt0) cc_final: 0.8419 (pp20) REVERT: A 403 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8863 (mt-10) REVERT: A 464 ASP cc_start: 0.8389 (t0) cc_final: 0.8038 (t70) REVERT: D 3 GLN cc_start: 0.8343 (pm20) cc_final: 0.8127 (pm20) REVERT: D 44 GLU cc_start: 0.8764 (tp30) cc_final: 0.8449 (tp30) REVERT: D 59 TYR cc_start: 0.9171 (m-80) cc_final: 0.8299 (m-80) REVERT: D 67 ARG cc_start: 0.9150 (mtm-85) cc_final: 0.8681 (mtm110) REVERT: D 76 LYS cc_start: 0.9590 (ptpp) cc_final: 0.9272 (ptpp) REVERT: D 77 ASN cc_start: 0.9092 (t0) cc_final: 0.8592 (t0) REVERT: D 80 TYR cc_start: 0.8554 (m-80) cc_final: 0.8136 (m-80) REVERT: D 82 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8515 (tm-30) REVERT: D 83 MET cc_start: 0.8702 (mmm) cc_final: 0.8412 (mmm) REVERT: D 121 GLN cc_start: 0.8808 (mp10) cc_final: 0.8352 (pm20) REVERT: E 44 GLU cc_start: 0.8872 (mp0) cc_final: 0.8243 (mp0) REVERT: E 46 GLU cc_start: 0.8145 (pm20) cc_final: 0.7628 (pm20) REVERT: E 76 LYS cc_start: 0.9417 (mtmm) cc_final: 0.9203 (mtmm) outliers start: 16 outliers final: 15 residues processed: 126 average time/residue: 0.1713 time to fit residues: 27.9081 Evaluate side-chains 129 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 113 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.108542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083587 restraints weight = 13986.881| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 4.37 r_work: 0.3129 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5358 Z= 0.137 Angle : 0.724 10.439 7287 Z= 0.367 Chirality : 0.046 0.228 753 Planarity : 0.004 0.041 950 Dihedral : 4.628 17.653 736 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.05 % Favored : 94.64 % Rotamer: Outliers : 2.86 % Allowed : 24.33 % Favored : 72.81 % 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: -1.35 (0.32), residues: 653 helix: -2.75 (0.61), residues: 55 sheet: 0.58 (0.40), residues: 185 loop : -1.40 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 PHE 0.012 0.001 PHE E 68 TYR 0.009 0.001 TYR B 491 ARG 0.006 0.000 ARG B 343 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 131) hydrogen bonds : angle 5.96103 ( 315) SS BOND : bond 0.00445 ( 12) SS BOND : angle 1.10578 ( 24) covalent geometry : bond 0.00322 ( 5346) covalent geometry : angle 0.72218 ( 7263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.32 seconds wall clock time: 65 minutes 27.85 seconds (3927.85 seconds total)