Starting phenix.real_space_refine on Fri Dec 27 13:56:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co9_45774/12_2024/9co9_45774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co9_45774/12_2024/9co9_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_45774/12_2024/9co9_45774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co9_45774/12_2024/9co9_45774.map" model { file = "/net/cci-nas-00/data/ceres_data/9co9_45774/12_2024/9co9_45774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co9_45774/12_2024/9co9_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-5532/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: 4.52, per 1000 atoms: 0.87 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: 1.35 Conformation dependent library (CDL) restraints added in 676.9 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: 0.56 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: 1.15 Time building geometry restraints manager: 1.52 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.890 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- 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 5346 Z= 0.378 Angle : 1.021 11.654 7263 Z= 0.610 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 *********************** 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 : 0.614 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: 0.2188 time to fit residues: 55.7644 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 : 0.681 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5346 Z= 0.239 Angle : 0.749 9.043 7263 Z= 0.383 Chirality : 0.048 0.175 753 Planarity : 0.005 0.047 950 Dihedral : 5.341 25.826 738 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.51 % Favored : 94.18 % Rotamer: Outliers : 2.15 % Allowed : 16.28 % Favored : 81.57 % 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: -1.89 (0.31), residues: 653 helix: -3.83 (0.46), residues: 55 sheet: 0.39 (0.42), residues: 172 loop : -1.70 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 449 HIS 0.003 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 *********************** 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 155 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 LEU cc_start: 0.7027 (tt) cc_final: 0.6452 (tt) REVERT: D 44 GLU cc_start: 0.7288 (tp30) cc_final: 0.7025 (tp30) REVERT: D 125 VAL cc_start: 0.8904 (t) cc_final: 0.8687 (p) REVERT: E 89 GLU cc_start: 0.8188 (pm20) cc_final: 0.7146 (pm20) REVERT: E 114 ASP cc_start: 0.7985 (t70) cc_final: 0.7591 (t0) outliers start: 12 outliers final: 8 residues processed: 152 average time/residue: 0.2088 time to fit residues: 40.0497 Evaluate side-chains 132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU 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 71 SER 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 32 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5346 Z= 0.209 Angle : 0.688 8.825 7263 Z= 0.354 Chirality : 0.046 0.161 753 Planarity : 0.005 0.042 950 Dihedral : 4.997 21.307 736 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.49 % Rotamer: Outliers : 2.68 % Allowed : 18.96 % Favored : 78.35 % 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: -1.77 (0.31), residues: 653 helix: -3.61 (0.46), residues: 55 sheet: 0.44 (0.41), residues: 182 loop : -1.67 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 433 HIS 0.005 0.001 HIS D 32 PHE 0.024 0.001 PHE E 68 TYR 0.035 0.001 TYR D 94 ARG 0.004 0.000 ARG D 67 *********************** 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 151 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 3 GLN cc_start: 0.8130 (mm110) cc_final: 0.7104 (mm-40) REVERT: E 114 ASP cc_start: 0.7976 (t70) cc_final: 0.7591 (t0) outliers start: 15 outliers final: 13 residues processed: 143 average time/residue: 0.1839 time to fit residues: 33.5979 Evaluate side-chains 133 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 71 SER Chi-restraints excluded: chain D residue 77 ASN 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 57 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.0000 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS D 77 ASN D 121 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5346 Z= 0.241 Angle : 0.706 8.300 7263 Z= 0.366 Chirality : 0.046 0.175 753 Planarity : 0.005 0.043 950 Dihedral : 5.288 31.991 736 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.36 % Favored : 94.33 % Rotamer: Outliers : 4.47 % Allowed : 18.43 % Favored : 77.10 % 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: -1.60 (0.32), residues: 653 helix: -3.31 (0.63), residues: 42 sheet: 0.49 (0.40), residues: 185 loop : -1.64 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 433 HIS 0.004 0.001 HIS B 515 PHE 0.014 0.001 PHE E 68 TYR 0.026 0.001 TYR D 59 ARG 0.004 0.000 ARG B 343 *********************** 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: 25 poor density : 124 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 LYS cc_start: 0.8289 (ttmt) cc_final: 0.8010 (ttmt) REVERT: E 114 ASP cc_start: 0.7843 (t70) cc_final: 0.7444 (t0) outliers start: 25 outliers final: 15 residues processed: 138 average time/residue: 0.2104 time to fit residues: 38.3531 Evaluate side-chains 136 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 B residue 458 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 68 PHE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 77 ASN 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 35 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.0270 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 0.0010 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN E 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5346 Z= 0.211 Angle : 0.710 8.572 7263 Z= 0.364 Chirality : 0.045 0.160 753 Planarity : 0.004 0.037 950 Dihedral : 4.898 21.398 736 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.90 % Favored : 94.79 % Rotamer: Outliers : 3.04 % Allowed : 20.21 % Favored : 76.74 % 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: -1.52 (0.32), residues: 653 helix: -3.45 (0.50), residues: 54 sheet: 0.56 (0.40), residues: 184 loop : -1.48 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.004 0.001 HIS D 32 PHE 0.013 0.001 PHE E 68 TYR 0.040 0.001 TYR D 94 ARG 0.005 0.000 ARG B 343 *********************** 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 145 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 114 ASP cc_start: 0.7809 (t70) cc_final: 0.7439 (t0) outliers start: 17 outliers final: 13 residues processed: 136 average time/residue: 0.2024 time to fit residues: 35.3837 Evaluate side-chains 133 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 THR 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 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 76 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5346 Z= 0.244 Angle : 0.722 8.534 7263 Z= 0.370 Chirality : 0.045 0.193 753 Planarity : 0.004 0.038 950 Dihedral : 4.919 21.426 736 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.49 % Rotamer: Outliers : 4.11 % Allowed : 20.93 % 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: -1.51 (0.32), residues: 653 helix: -3.34 (0.57), residues: 48 sheet: 0.49 (0.40), residues: 186 loop : -1.49 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.004 0.001 HIS B 515 PHE 0.020 0.001 PHE E 68 TYR 0.031 0.001 TYR D 59 ARG 0.005 0.000 ARG D 38 *********************** 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: 23 poor density : 120 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 GLN cc_start: 0.7108 (pm20) cc_final: 0.6714 (pm20) REVERT: E 44 GLU cc_start: 0.7914 (mp0) cc_final: 0.7563 (mp0) REVERT: E 114 ASP cc_start: 0.7833 (t70) cc_final: 0.7453 (t0) outliers start: 23 outliers final: 15 residues processed: 134 average time/residue: 0.1732 time to fit residues: 29.8577 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 : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 458 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 38 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 77 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 37 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5346 Z= 0.228 Angle : 0.739 12.286 7263 Z= 0.375 Chirality : 0.046 0.173 753 Planarity : 0.004 0.038 950 Dihedral : 4.910 20.971 736 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.51 % Favored : 94.18 % Rotamer: Outliers : 3.22 % Allowed : 23.26 % Favored : 73.52 % 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: -1.53 (0.32), residues: 653 helix: -3.30 (0.54), residues: 54 sheet: 0.65 (0.42), residues: 166 loop : -1.47 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 PHE 0.018 0.001 PHE E 68 TYR 0.032 0.001 TYR D 118 ARG 0.003 0.000 ARG D 38 *********************** 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 138 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8691 (p0) cc_final: 0.8491 (p0) REVERT: D 3 GLN cc_start: 0.7111 (pm20) cc_final: 0.6716 (pm20) REVERT: E 73 ASP cc_start: 0.8495 (t0) cc_final: 0.8155 (t0) REVERT: E 114 ASP cc_start: 0.7879 (t70) cc_final: 0.7498 (t0) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.1804 time to fit residues: 29.8955 Evaluate side-chains 131 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 458 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 4 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 77 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5346 Z= 0.255 Angle : 0.745 11.248 7263 Z= 0.379 Chirality : 0.046 0.189 753 Planarity : 0.004 0.041 950 Dihedral : 4.965 21.495 736 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.05 % Favored : 94.64 % Rotamer: Outliers : 3.40 % Allowed : 24.15 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.32), residues: 653 helix: -3.31 (0.53), residues: 54 sheet: 0.50 (0.41), residues: 176 loop : -1.50 (0.28), residues: 423 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 A 389 TYR 0.030 0.001 TYR D 59 ARG 0.015 0.001 ARG D 67 *********************** 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 135 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7892 (p90) REVERT: A 425 ASP cc_start: 0.8771 (p0) cc_final: 0.8530 (p0) REVERT: D 3 GLN cc_start: 0.7069 (pm20) cc_final: 0.6759 (pm20) REVERT: E 73 ASP cc_start: 0.8432 (t0) cc_final: 0.8046 (t0) REVERT: E 114 ASP cc_start: 0.7869 (t70) cc_final: 0.7447 (t0) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.2353 time to fit residues: 38.8470 Evaluate side-chains 127 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 458 LEU 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 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 E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5346 Z= 0.243 Angle : 0.756 10.542 7263 Z= 0.385 Chirality : 0.046 0.182 753 Planarity : 0.004 0.041 950 Dihedral : 4.939 20.905 736 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.49 % Rotamer: Outliers : 3.22 % Allowed : 24.87 % Favored : 71.91 % 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: -1.58 (0.32), residues: 653 helix: -3.25 (0.55), residues: 54 sheet: 0.54 (0.41), residues: 176 loop : -1.53 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 PHE 0.008 0.001 PHE A 389 TYR 0.031 0.001 TYR D 59 ARG 0.009 0.001 ARG D 67 *********************** 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 134 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8803 (p0) cc_final: 0.8544 (p0) REVERT: D 3 GLN cc_start: 0.6854 (pm20) cc_final: 0.6614 (pm20) REVERT: E 89 GLU cc_start: 0.8508 (pm20) cc_final: 0.8077 (pm20) REVERT: E 114 ASP cc_start: 0.7815 (t70) cc_final: 0.7410 (t0) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.2153 time to fit residues: 35.8632 Evaluate side-chains 124 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 458 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 58 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 0.0470 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5346 Z= 0.250 Angle : 0.791 10.408 7263 Z= 0.402 Chirality : 0.047 0.183 753 Planarity : 0.004 0.040 950 Dihedral : 5.162 28.702 736 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.36 % Favored : 94.33 % Rotamer: Outliers : 2.68 % Allowed : 25.58 % Favored : 71.74 % 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: -1.54 (0.32), residues: 653 helix: -3.23 (0.55), residues: 54 sheet: 0.58 (0.41), residues: 176 loop : -1.51 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS D 105 PHE 0.009 0.001 PHE A 389 TYR 0.032 0.001 TYR D 59 ARG 0.006 0.001 ARG D 67 ********************** 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 125 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8796 (p0) cc_final: 0.8523 (p0) REVERT: E 114 ASP cc_start: 0.7829 (t70) cc_final: 0.7482 (t0) outliers start: 15 outliers final: 15 residues processed: 120 average time/residue: 0.1808 time to fit residues: 28.2799 Evaluate side-chains 119 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 458 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 38 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.108750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082744 restraints weight = 13760.527| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.35 r_work: 0.3141 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5346 Z= 0.240 Angle : 0.779 9.808 7263 Z= 0.397 Chirality : 0.047 0.177 753 Planarity : 0.004 0.040 950 Dihedral : 4.988 28.104 736 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.05 % Favored : 94.64 % Rotamer: Outliers : 2.68 % Allowed : 25.58 % Favored : 71.74 % 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: -1.49 (0.32), residues: 653 helix: -3.07 (0.56), residues: 55 sheet: 0.53 (0.41), residues: 176 loop : -1.44 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 PHE 0.008 0.001 PHE A 389 TYR 0.029 0.001 TYR D 59 ARG 0.006 0.001 ARG D 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.54 seconds wall clock time: 38 minutes 11.91 seconds (2291.91 seconds total)