Starting phenix.real_space_refine on Wed Sep 17 05:29:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co9_45774/09_2025/9co9_45774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co9_45774/09_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_45774/09_2025/9co9_45774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co9_45774/09_2025/9co9_45774.map" model { file = "/net/cci-nas-00/data/ceres_data/9co9_45774/09_2025/9co9_45774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co9_45774/09_2025/9co9_45774.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.31 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: 0.42 Conformation dependent library (CDL) restraints added in 220.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.20 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: 0.71 Time building geometry restraints manager: 0.59 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: 5.070 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG D 67 TYR 0.031 0.002 TYR D 110 PHE 0.032 0.002 PHE A 335 TRP 0.040 0.003 TRP A 449 HIS 0.007 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 5346) covalent geometry : angle 1.02104 ( 7263) SS BOND : bond 0.00906 ( 12) SS BOND : angle 1.80048 ( 24) hydrogen bonds : bond 0.27164 ( 131) hydrogen bonds : angle 9.56907 ( 315) *********************** 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 : 0.218 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: 0.1025 time to fit residues: 26.3412 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 : 0.201 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN B 501 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082587 restraints weight = 14025.563| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.43 r_work: 0.3150 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5358 Z= 0.172 Angle : 0.759 9.116 7287 Z= 0.388 Chirality : 0.047 0.173 753 Planarity : 0.005 0.050 950 Dihedral : 5.451 26.941 738 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.49 % Rotamer: Outliers : 1.97 % Allowed : 15.56 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.31), residues: 653 helix: -3.81 (0.46), residues: 55 sheet: 0.37 (0.40), residues: 181 loop : -1.72 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 38 TYR 0.024 0.002 TYR D 110 PHE 0.022 0.002 PHE E 68 TRP 0.017 0.002 TRP A 449 HIS 0.004 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5346) covalent geometry : angle 0.74896 ( 7263) SS BOND : bond 0.00604 ( 12) SS BOND : angle 2.26252 ( 24) hydrogen bonds : bond 0.03933 ( 131) hydrogen bonds : angle 6.84697 ( 315) *********************** 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: 11 poor density : 141 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8404 (tpp80) REVERT: B 462 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 403 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8751 (mt-10) REVERT: A 464 ASP cc_start: 0.8461 (t0) cc_final: 0.8168 (t0) REVERT: A 496 THR cc_start: 0.8881 (p) cc_final: 0.8542 (t) REVERT: A 514 LEU cc_start: 0.7280 (tt) cc_final: 0.6677 (tt) REVERT: D 36 TRP cc_start: 0.8109 (m100) cc_final: 0.7862 (m100) REVERT: D 44 GLU cc_start: 0.8259 (tp30) cc_final: 0.7573 (tp30) REVERT: D 59 TYR cc_start: 0.8884 (m-80) cc_final: 0.8199 (m-80) REVERT: D 77 ASN cc_start: 0.8852 (t0) cc_final: 0.7879 (t0) REVERT: D 95 TYR cc_start: 0.7312 (m-80) cc_final: 0.7094 (m-80) REVERT: D 115 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8007 (p0) REVERT: E 13 GLN cc_start: 0.8465 (mm110) cc_final: 0.8218 (mm-40) REVERT: E 19 ARG cc_start: 0.9064 (ttt-90) cc_final: 0.8669 (ttt-90) outliers start: 11 outliers final: 7 residues processed: 150 average time/residue: 0.0900 time to fit residues: 17.0365 Evaluate side-chains 130 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 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 = 0.3726 r_free = 0.3726 target = 0.107748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081676 restraints weight = 14008.383| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.38 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: 0.8161 moved from start: 0.4360 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 : 0.696 8.554 7287 Z= 0.356 Chirality : 0.046 0.171 753 Planarity : 0.005 0.047 950 Dihedral : 5.103 23.184 736 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.67 % Favored : 94.03 % Rotamer: Outliers : 3.04 % Allowed : 16.99 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.31), residues: 653 helix: -3.42 (0.61), residues: 41 sheet: 0.30 (0.40), residues: 184 loop : -1.79 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 67 TYR 0.032 0.001 TYR D 94 PHE 0.027 0.001 PHE E 68 TRP 0.012 0.001 TRP A 433 HIS 0.004 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5346) covalent geometry : angle 0.68765 ( 7263) SS BOND : bond 0.00508 ( 12) SS BOND : angle 2.01565 ( 24) hydrogen bonds : bond 0.03570 ( 131) hydrogen bonds : angle 6.54222 ( 315) *********************** 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 150 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 ARG cc_start: 0.8846 (ptp90) cc_final: 0.8608 (ptp90) REVERT: B 395 ASP cc_start: 0.9059 (p0) cc_final: 0.8808 (p0) REVERT: A 403 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8836 (mt-10) REVERT: A 464 ASP cc_start: 0.8414 (t0) cc_final: 0.8181 (t0) REVERT: D 19 ARG cc_start: 0.9216 (ttm-80) cc_final: 0.8955 (ttt90) REVERT: D 44 GLU cc_start: 0.8354 (tp30) cc_final: 0.7808 (tp30) REVERT: D 59 TYR cc_start: 0.8881 (m-80) cc_final: 0.8309 (m-80) REVERT: D 77 ASN cc_start: 0.8673 (t0) cc_final: 0.7747 (t0) REVERT: D 109 TYR cc_start: 0.8697 (t80) cc_final: 0.8462 (t80) REVERT: D 113 ASP cc_start: 0.8498 (m-30) cc_final: 0.7811 (t0) REVERT: E 3 GLN cc_start: 0.8832 (mm110) cc_final: 0.7557 (mm-40) outliers start: 17 outliers final: 14 residues processed: 142 average time/residue: 0.0756 time to fit residues: 13.9658 Evaluate side-chains 134 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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 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 79 VAL Chi-restraints excluded: chain E residue 2 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 56 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 E 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.108412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082158 restraints weight = 13785.599| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 4.41 r_work: 0.3136 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4730 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= 0.137 Angle : 0.690 8.527 7287 Z= 0.351 Chirality : 0.045 0.173 753 Planarity : 0.004 0.038 950 Dihedral : 5.143 30.366 736 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.90 % Favored : 94.79 % Rotamer: Outliers : 4.47 % Allowed : 17.17 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.32), residues: 653 helix: -3.46 (0.52), residues: 54 sheet: 0.30 (0.39), residues: 193 loop : -1.55 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 67 TYR 0.014 0.001 TYR D 118 PHE 0.015 0.001 PHE E 68 TRP 0.009 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5346) covalent geometry : angle 0.68381 ( 7263) SS BOND : bond 0.00483 ( 12) SS BOND : angle 1.69806 ( 24) hydrogen bonds : bond 0.03095 ( 131) hydrogen bonds : angle 6.29359 ( 315) *********************** 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 : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 ASP cc_start: 0.9102 (p0) cc_final: 0.8594 (p0) REVERT: A 403 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8845 (mt-10) REVERT: A 464 ASP cc_start: 0.8438 (t0) cc_final: 0.8115 (t0) REVERT: D 19 ARG cc_start: 0.9195 (ttm-80) cc_final: 0.8887 (ttt90) REVERT: D 44 GLU cc_start: 0.8362 (tp30) cc_final: 0.7983 (tp30) REVERT: D 59 TYR cc_start: 0.8897 (m-80) cc_final: 0.8286 (m-80) REVERT: D 77 ASN cc_start: 0.8795 (t0) cc_final: 0.7901 (t0) REVERT: D 109 TYR cc_start: 0.8654 (t80) cc_final: 0.8424 (t80) REVERT: D 113 ASP cc_start: 0.8534 (m-30) cc_final: 0.7761 (t0) REVERT: D 117 TYR cc_start: 0.8478 (t80) cc_final: 0.7864 (t80) REVERT: E 1 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6499 (pp30) REVERT: E 3 GLN cc_start: 0.8670 (mm110) cc_final: 0.8325 (mm110) REVERT: E 87 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8523 (mtmm) outliers start: 25 outliers final: 13 residues processed: 137 average time/residue: 0.0757 time to fit residues: 13.5273 Evaluate side-chains 134 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU 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 68 PHE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 1 GLN 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 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.0370 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.108260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083599 restraints weight = 14123.764| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 4.40 r_work: 0.3136 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5358 Z= 0.130 Angle : 0.697 11.219 7287 Z= 0.350 Chirality : 0.045 0.163 753 Planarity : 0.004 0.037 950 Dihedral : 4.786 19.469 736 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.59 % Favored : 95.10 % Rotamer: Outliers : 3.22 % Allowed : 19.14 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.32), residues: 653 helix: -3.41 (0.52), residues: 54 sheet: 0.32 (0.39), residues: 195 loop : -1.45 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.014 0.001 TYR D 111 PHE 0.011 0.001 PHE D 37 TRP 0.010 0.001 TRP D 36 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5346) covalent geometry : angle 0.69452 ( 7263) SS BOND : bond 0.00454 ( 12) SS BOND : angle 1.21436 ( 24) hydrogen bonds : bond 0.03019 ( 131) hydrogen bonds : angle 6.12066 ( 315) *********************** 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: 18 poor density : 127 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 ASP cc_start: 0.8932 (p0) cc_final: 0.8554 (p0) REVERT: B 512 GLU cc_start: 0.8841 (pt0) cc_final: 0.8526 (pp20) REVERT: A 403 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8839 (mt-10) REVERT: A 464 ASP cc_start: 0.8391 (t0) cc_final: 0.8085 (t0) REVERT: D 18 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7842 (pp) REVERT: D 19 ARG cc_start: 0.9157 (ttm-80) cc_final: 0.8772 (ttt90) REVERT: D 44 GLU cc_start: 0.8436 (tp30) cc_final: 0.8100 (tp30) REVERT: D 59 TYR cc_start: 0.9035 (m-80) cc_final: 0.8500 (m-80) REVERT: D 77 ASN cc_start: 0.8856 (t0) cc_final: 0.7973 (t0) REVERT: D 83 MET cc_start: 0.8571 (mmm) cc_final: 0.7540 (tpt) REVERT: D 94 TYR cc_start: 0.8167 (m-10) cc_final: 0.7956 (m-10) REVERT: D 109 TYR cc_start: 0.8628 (t80) cc_final: 0.8407 (t80) REVERT: D 113 ASP cc_start: 0.8535 (m-30) cc_final: 0.7730 (t0) REVERT: D 117 TYR cc_start: 0.8484 (t80) cc_final: 0.7863 (t80) REVERT: E 44 GLU cc_start: 0.8774 (mp0) cc_final: 0.8137 (mp0) REVERT: E 46 GLU cc_start: 0.7841 (pm20) cc_final: 0.7361 (pm20) REVERT: E 73 ASP cc_start: 0.9185 (t0) cc_final: 0.8957 (t0) outliers start: 18 outliers final: 13 residues processed: 137 average time/residue: 0.0749 time to fit residues: 13.4151 Evaluate side-chains 137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 506 VAL 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 68 PHE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 2 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 60 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.0010 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083392 restraints weight = 14106.401| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.43 r_work: 0.3136 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5358 Z= 0.130 Angle : 0.688 9.879 7287 Z= 0.347 Chirality : 0.045 0.165 753 Planarity : 0.004 0.038 950 Dihedral : 4.718 18.856 736 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.44 % Favored : 95.25 % Rotamer: Outliers : 3.76 % Allowed : 19.32 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.32), residues: 653 helix: -3.36 (0.53), residues: 54 sheet: 0.35 (0.39), residues: 195 loop : -1.37 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.014 0.001 TYR D 118 PHE 0.016 0.001 PHE E 68 TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5346) covalent geometry : angle 0.68579 ( 7263) SS BOND : bond 0.00462 ( 12) SS BOND : angle 1.12588 ( 24) hydrogen bonds : bond 0.03003 ( 131) hydrogen bonds : angle 6.00319 ( 315) *********************** 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 147 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 ASP cc_start: 0.8938 (p0) cc_final: 0.8537 (p0) REVERT: B 512 GLU cc_start: 0.8881 (pt0) cc_final: 0.8546 (pp20) REVERT: A 403 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8845 (mt-10) REVERT: A 464 ASP cc_start: 0.8386 (t0) cc_final: 0.8072 (t0) REVERT: D 19 ARG cc_start: 0.9148 (ttm-80) cc_final: 0.8699 (ttt90) REVERT: D 44 GLU cc_start: 0.8361 (tp30) cc_final: 0.8054 (tp30) REVERT: D 59 TYR cc_start: 0.9092 (m-80) cc_final: 0.8459 (m-80) REVERT: D 67 ARG cc_start: 0.9150 (mtm-85) cc_final: 0.8488 (mtm-85) REVERT: D 77 ASN cc_start: 0.8921 (t0) cc_final: 0.8110 (t0) REVERT: D 83 MET cc_start: 0.8602 (mmm) cc_final: 0.7577 (tpt) REVERT: D 94 TYR cc_start: 0.8107 (m-10) cc_final: 0.7905 (m-10) REVERT: D 109 TYR cc_start: 0.8614 (t80) cc_final: 0.8400 (t80) REVERT: D 113 ASP cc_start: 0.8485 (m-30) cc_final: 0.7503 (t0) REVERT: D 115 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7596 (p0) REVERT: D 117 TYR cc_start: 0.8475 (t80) cc_final: 0.7883 (t80) REVERT: E 3 GLN cc_start: 0.8722 (mm110) cc_final: 0.8412 (mm110) REVERT: E 44 GLU cc_start: 0.8809 (mp0) cc_final: 0.8218 (mp0) REVERT: E 46 GLU cc_start: 0.7937 (pm20) cc_final: 0.7431 (pm20) outliers start: 21 outliers final: 15 residues processed: 138 average time/residue: 0.0780 time to fit residues: 13.9944 Evaluate side-chains 135 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 506 VAL 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 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 Chi-restraints excluded: chain E residue 76 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.107796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083168 restraints weight = 13988.888| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.45 r_work: 0.3123 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5252 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= 0.144 Angle : 0.695 10.411 7287 Z= 0.354 Chirality : 0.045 0.171 753 Planarity : 0.004 0.039 950 Dihedral : 4.706 19.141 736 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.36 % Favored : 94.33 % Rotamer: Outliers : 3.94 % Allowed : 21.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.32), residues: 653 helix: -3.31 (0.54), residues: 54 sheet: 0.36 (0.40), residues: 185 loop : -1.34 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.012 0.001 TYR D 118 PHE 0.010 0.001 PHE B 397 TRP 0.008 0.001 TRP D 36 HIS 0.004 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5346) covalent geometry : angle 0.69313 ( 7263) SS BOND : bond 0.00437 ( 12) SS BOND : angle 1.16027 ( 24) hydrogen bonds : bond 0.03007 ( 131) hydrogen bonds : angle 5.94485 ( 315) *********************** 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 146 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8195 (t80) cc_final: 0.7693 (t80) REVERT: B 395 ASP cc_start: 0.8952 (p0) cc_final: 0.8550 (p0) REVERT: B 462 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 512 GLU cc_start: 0.8976 (pt0) cc_final: 0.8478 (pp20) REVERT: A 403 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8853 (mt-10) REVERT: A 464 ASP cc_start: 0.8394 (t0) cc_final: 0.8061 (t0) REVERT: D 18 LEU cc_start: 0.8120 (pp) cc_final: 0.7866 (pt) REVERT: D 19 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8646 (ttt90) REVERT: D 20 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8751 (mp) REVERT: D 44 GLU cc_start: 0.8436 (tp30) cc_final: 0.8072 (tp30) REVERT: D 59 TYR cc_start: 0.9077 (m-80) cc_final: 0.8492 (m-80) REVERT: D 67 ARG cc_start: 0.9171 (mtm-85) cc_final: 0.8678 (mtm110) REVERT: D 77 ASN cc_start: 0.8846 (t0) cc_final: 0.8130 (t0) REVERT: D 82 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8509 (tm-30) REVERT: D 83 MET cc_start: 0.8688 (mmm) cc_final: 0.8481 (mmm) REVERT: D 94 TYR cc_start: 0.8197 (m-10) cc_final: 0.7839 (m-10) REVERT: D 117 TYR cc_start: 0.8527 (t80) cc_final: 0.7879 (t80) REVERT: D 121 GLN cc_start: 0.8836 (mp10) cc_final: 0.8629 (mp10) REVERT: E 3 GLN cc_start: 0.8783 (mm110) cc_final: 0.8347 (mm-40) REVERT: E 44 GLU cc_start: 0.8836 (mp0) cc_final: 0.8249 (mp0) REVERT: E 46 GLU cc_start: 0.8022 (pm20) cc_final: 0.7493 (pm20) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.0768 time to fit residues: 13.8027 Evaluate side-chains 143 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 506 VAL 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 511 PHE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain D residue 20 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 E residue 51 ILE Chi-restraints excluded: chain E residue 74 ASN 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 19 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.106813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080605 restraints weight = 13880.605| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.37 r_work: 0.3104 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5358 Z= 0.169 Angle : 0.721 12.173 7287 Z= 0.365 Chirality : 0.046 0.185 753 Planarity : 0.004 0.041 950 Dihedral : 4.833 22.119 736 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.36 % Favored : 94.33 % Rotamer: Outliers : 3.40 % Allowed : 22.54 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.32), residues: 653 helix: -3.29 (0.54), residues: 54 sheet: 0.34 (0.40), residues: 186 loop : -1.40 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.013 0.001 TYR D 118 PHE 0.010 0.001 PHE B 397 TRP 0.008 0.001 TRP A 433 HIS 0.005 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5346) covalent geometry : angle 0.71919 ( 7263) SS BOND : bond 0.00464 ( 12) SS BOND : angle 1.19767 ( 24) hydrogen bonds : bond 0.03087 ( 131) hydrogen bonds : angle 5.94096 ( 315) *********************** 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 137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8290 (t80) cc_final: 0.7663 (t80) REVERT: B 390 THR cc_start: 0.9409 (p) cc_final: 0.8921 (p) REVERT: B 395 ASP cc_start: 0.8986 (p0) cc_final: 0.8606 (p0) REVERT: B 462 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 389 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8270 (p90) REVERT: A 403 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8884 (mt-10) REVERT: A 464 ASP cc_start: 0.8371 (t0) cc_final: 0.7865 (t0) REVERT: D 18 LEU cc_start: 0.8189 (pp) cc_final: 0.7887 (pt) REVERT: D 19 ARG cc_start: 0.9042 (ttm-80) cc_final: 0.8551 (ttt90) REVERT: D 59 TYR cc_start: 0.9031 (m-80) cc_final: 0.8502 (m-80) REVERT: D 67 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8682 (mtm110) REVERT: D 77 ASN cc_start: 0.8957 (t0) cc_final: 0.8258 (t0) REVERT: D 82 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8560 (tm-30) REVERT: D 94 TYR cc_start: 0.8152 (m-10) cc_final: 0.7794 (m-10) REVERT: D 117 TYR cc_start: 0.8548 (t80) cc_final: 0.7887 (t80) REVERT: E 44 GLU cc_start: 0.8892 (mp0) cc_final: 0.8338 (mp0) REVERT: E 46 GLU cc_start: 0.8126 (pm20) cc_final: 0.7536 (pm20) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 0.0780 time to fit residues: 13.2964 Evaluate side-chains 128 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU 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 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 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 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 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 = 0.3700 r_free = 0.3700 target = 0.106086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081451 restraints weight = 13863.583| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.40 r_work: 0.3059 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5358 Z= 0.210 Angle : 0.785 11.891 7287 Z= 0.400 Chirality : 0.047 0.184 753 Planarity : 0.004 0.042 950 Dihedral : 5.233 28.509 736 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.13 % Favored : 93.57 % Rotamer: Outliers : 3.22 % Allowed : 22.18 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.32), residues: 653 helix: -3.30 (0.54), residues: 54 sheet: 0.39 (0.39), residues: 192 loop : -1.57 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.017 0.001 TYR D 94 PHE 0.010 0.001 PHE B 397 TRP 0.017 0.002 TRP D 36 HIS 0.006 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 5346) covalent geometry : angle 0.78023 ( 7263) SS BOND : bond 0.00516 ( 12) SS BOND : angle 1.68051 ( 24) hydrogen bonds : bond 0.03170 ( 131) hydrogen bonds : angle 5.97226 ( 315) *********************** 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 : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8381 (t80) cc_final: 0.7655 (t80) REVERT: B 390 THR cc_start: 0.9363 (p) cc_final: 0.8939 (p) REVERT: B 395 ASP cc_start: 0.9011 (p0) cc_final: 0.8655 (p0) REVERT: B 462 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 389 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8199 (p90) REVERT: A 403 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8924 (mt-10) REVERT: A 464 ASP cc_start: 0.8415 (t0) cc_final: 0.7882 (t0) REVERT: D 18 LEU cc_start: 0.7914 (pp) cc_final: 0.7710 (pt) REVERT: D 59 TYR cc_start: 0.9061 (m-80) cc_final: 0.8623 (m-80) REVERT: D 67 ARG cc_start: 0.9198 (mtm-85) cc_final: 0.8958 (mtm-85) REVERT: D 77 ASN cc_start: 0.9049 (t0) cc_final: 0.8332 (t0) REVERT: D 82 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8623 (tm-30) REVERT: D 117 TYR cc_start: 0.8672 (t80) cc_final: 0.7960 (t80) REVERT: E 44 GLU cc_start: 0.8983 (mp0) cc_final: 0.8438 (mp0) REVERT: E 46 GLU cc_start: 0.8252 (pm20) cc_final: 0.7666 (pm20) REVERT: E 76 LYS cc_start: 0.9441 (mtmm) cc_final: 0.9212 (mtmm) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 0.0792 time to fit residues: 13.2287 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 : 0.216 ------------------------------------------------------------------------------- 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 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 520 VAL 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 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 48 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 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 = 0.3710 r_free = 0.3710 target = 0.106971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080811 restraints weight = 14185.059| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.34 r_work: 0.3101 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5358 Z= 0.158 Angle : 0.765 11.798 7287 Z= 0.387 Chirality : 0.046 0.173 753 Planarity : 0.004 0.042 950 Dihedral : 4.980 18.104 736 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.51 % Favored : 94.18 % Rotamer: Outliers : 2.68 % Allowed : 24.15 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.32), residues: 653 helix: -3.16 (0.56), residues: 54 sheet: 0.28 (0.39), residues: 194 loop : -1.52 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 343 TYR 0.016 0.001 TYR D 118 PHE 0.009 0.001 PHE B 397 TRP 0.009 0.001 TRP B 350 HIS 0.006 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5346) covalent geometry : angle 0.76309 ( 7263) SS BOND : bond 0.00491 ( 12) SS BOND : angle 1.23533 ( 24) hydrogen bonds : bond 0.03055 ( 131) hydrogen bonds : angle 5.97408 ( 315) ********************** 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: 15 poor density : 117 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 PHE cc_start: 0.8276 (t80) cc_final: 0.7634 (t80) REVERT: B 390 THR cc_start: 0.9345 (p) cc_final: 0.9053 (p) REVERT: B 395 ASP cc_start: 0.8958 (p0) cc_final: 0.8564 (p0) REVERT: B 462 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 512 GLU cc_start: 0.9011 (pt0) cc_final: 0.8459 (pp20) REVERT: A 389 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8377 (p90) REVERT: A 403 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8879 (mt-10) REVERT: A 464 ASP cc_start: 0.8395 (t0) cc_final: 0.7898 (t0) REVERT: D 18 LEU cc_start: 0.8009 (pp) cc_final: 0.7736 (pt) REVERT: D 19 ARG cc_start: 0.9109 (ttm-80) cc_final: 0.8719 (ttt90) REVERT: D 59 TYR cc_start: 0.9136 (m-80) cc_final: 0.8377 (m-80) REVERT: D 67 ARG cc_start: 0.9207 (mtm-85) cc_final: 0.8736 (mtm-85) REVERT: D 77 ASN cc_start: 0.9060 (t0) cc_final: 0.8368 (t0) REVERT: D 82 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8527 (tm-30) REVERT: D 117 TYR cc_start: 0.8610 (t80) cc_final: 0.7974 (t80) REVERT: E 44 GLU cc_start: 0.8924 (mp0) cc_final: 0.8433 (mp0) REVERT: E 46 GLU cc_start: 0.8241 (pm20) cc_final: 0.7620 (pm20) REVERT: E 76 LYS cc_start: 0.9410 (mtmm) cc_final: 0.9182 (mtmm) outliers start: 15 outliers final: 12 residues processed: 129 average time/residue: 0.0825 time to fit residues: 13.7576 Evaluate side-chains 128 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU 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 520 VAL 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 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 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 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 = 0.3725 r_free = 0.3725 target = 0.107743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.081517 restraints weight = 14337.803| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.38 r_work: 0.3117 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5654 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= 0.143 Angle : 0.758 11.710 7287 Z= 0.381 Chirality : 0.046 0.169 753 Planarity : 0.004 0.041 950 Dihedral : 4.831 17.927 736 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.49 % Rotamer: Outliers : 2.86 % Allowed : 24.15 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.32), residues: 653 helix: -2.93 (0.58), residues: 55 sheet: 0.30 (0.40), residues: 184 loop : -1.47 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 343 TYR 0.016 0.001 TYR D 118 PHE 0.009 0.001 PHE B 397 TRP 0.010 0.001 TRP B 350 HIS 0.004 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5346) covalent geometry : angle 0.75639 ( 7263) SS BOND : bond 0.00452 ( 12) SS BOND : angle 1.12517 ( 24) hydrogen bonds : bond 0.02985 ( 131) hydrogen bonds : angle 5.90854 ( 315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.03 seconds wall clock time: 32 minutes 42.89 seconds (1962.89 seconds total)