Starting phenix.real_space_refine on Sat May 10 05:57:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co7_45772/05_2025/9co7_45772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co7_45772/05_2025/9co7_45772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9co7_45772/05_2025/9co7_45772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co7_45772/05_2025/9co7_45772.map" model { file = "/net/cci-nas-00/data/ceres_data/9co7_45772/05_2025/9co7_45772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co7_45772/05_2025/9co7_45772.cif" } resolution = 3.32 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 3312 2.51 5 N 892 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5220 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1632 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} 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} Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1632 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} 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} Time building chain proxies: 3.80, per 1000 atoms: 0.73 Number of scatterers: 5220 At special positions: 0 Unit cell: (82.336, 109.781, 120.405, 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 990 8.00 N 892 7.00 C 3312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 520 " distance=2.05 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 50 " - pdb=" SG CYS E 104 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.05 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 520 " distance=2.04 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 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: 1.09 Conformation dependent library (CDL) restraints added in 591.9 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 8.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.604A pdb=" N TRP B 348 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.787A pdb=" N THR E 91 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.594A pdb=" N TRP A 348 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 5.081A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.719A pdb=" N ASP D 90 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 4.056A 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 sheet with id=AA1, first strand: chain 'B' and resid 349 through 352 removed outlier: 3.565A pdb=" N ASN B 349 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 389 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLU B 511 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AA3, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.331A pdb=" N THR E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS E 50 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 351 removed outlier: 3.686A pdb=" N ASN A 349 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 392 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A 389 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU A 511 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 447 through 449 Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.592A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'D' and resid 59 through 60 removed outlier: 3.835A pdb=" N CYS D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS D 50 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR D 34 " --> pdb=" O CYS D 50 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 309 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: 1.19 Time building geometry restraints manager: 1.32 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: 1702 1.35 - 1.48: 1495 1.48 - 1.61: 2133 1.61 - 1.74: 0 1.74 - 1.87: 28 Bond restraints: 5358 Sorted by residual: bond pdb=" CA SER E 128 " pdb=" CB SER E 128 " ideal model delta sigma weight residual 1.542 1.501 0.041 8.90e-03 1.26e+04 2.16e+01 bond pdb=" N VAL E 127 " pdb=" CA VAL E 127 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.30e-02 5.92e+03 5.65e+00 bond pdb=" N SER E 128 " pdb=" CA SER E 128 " ideal model delta sigma weight residual 1.460 1.484 -0.024 1.02e-02 9.61e+03 5.55e+00 bond pdb=" CA THR A 328 " pdb=" C THR A 328 " ideal model delta sigma weight residual 1.525 1.505 0.020 1.02e-02 9.61e+03 3.91e+00 bond pdb=" CB CYS A 427 " pdb=" SG CYS A 427 " ideal model delta sigma weight residual 1.808 1.869 -0.061 3.30e-02 9.18e+02 3.37e+00 ... (remaining 5353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 6847 1.98 - 3.97: 339 3.97 - 5.95: 61 5.95 - 7.93: 20 7.93 - 9.92: 13 Bond angle restraints: 7280 Sorted by residual: angle pdb=" C SER D 53 " pdb=" CA SER D 53 " pdb=" CB SER D 53 " ideal model delta sigma weight residual 116.54 109.53 7.01 1.15e+00 7.56e-01 3.72e+01 angle pdb=" N GLY D 122 " pdb=" CA GLY D 122 " pdb=" C GLY D 122 " ideal model delta sigma weight residual 112.33 117.93 -5.60 1.21e+00 6.83e-01 2.14e+01 angle pdb=" C LEU D 29 " pdb=" N HIS D 30 " pdb=" CA HIS D 30 " ideal model delta sigma weight residual 121.54 130.07 -8.53 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C THR B 388 " pdb=" N ASN B 389 " pdb=" CA ASN B 389 " ideal model delta sigma weight residual 121.54 129.50 -7.96 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C LEU E 29 " pdb=" N HIS E 30 " pdb=" CA HIS E 30 " ideal model delta sigma weight residual 122.61 128.97 -6.36 1.56e+00 4.11e-01 1.66e+01 ... (remaining 7275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 2774 16.37 - 32.73: 316 32.73 - 49.09: 47 49.09 - 65.46: 6 65.46 - 81.82: 7 Dihedral angle restraints: 3150 sinusoidal: 1226 harmonic: 1924 Sorted by residual: dihedral pdb=" CB CYS B 475 " pdb=" SG CYS B 475 " pdb=" SG CYS B 483 " pdb=" CB CYS B 483 " ideal model delta sinusoidal sigma weight residual 93.00 11.70 81.30 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 475 " pdb=" SG CYS A 475 " pdb=" SG CYS A 483 " pdb=" CB CYS A 483 " ideal model delta sinusoidal sigma weight residual 93.00 15.11 77.89 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual 93.00 48.02 44.98 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 3147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 542 0.057 - 0.114: 173 0.114 - 0.171: 37 0.171 - 0.227: 11 0.227 - 0.284: 1 Chirality restraints: 764 Sorted by residual: chirality pdb=" CB ILE D 70 " pdb=" CA ILE D 70 " pdb=" CG1 ILE D 70 " pdb=" CG2 ILE D 70 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA VAL E 127 " pdb=" N VAL E 127 " pdb=" C VAL E 127 " pdb=" CB VAL E 127 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE A 321 " pdb=" CA ILE A 321 " pdb=" CG1 ILE A 321 " pdb=" CG2 ILE A 321 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 761 not shown) Planarity restraints: 958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 13 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO E 14 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 117 " -0.023 2.00e-02 2.50e+03 1.88e-02 7.07e+00 pdb=" CG TYR D 117 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR D 117 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 117 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 117 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 117 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 117 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 65 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" CD GLU D 65 " 0.044 2.00e-02 2.50e+03 pdb=" OE1 GLU D 65 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU D 65 " -0.015 2.00e-02 2.50e+03 ... (remaining 955 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 447 2.75 - 3.29: 4923 3.29 - 3.83: 8137 3.83 - 4.36: 9328 4.36 - 4.90: 16416 Nonbonded interactions: 39251 Sorted by model distance: nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 2.215 3.040 nonbonded pdb=" OD2 ASP A 393 " pdb=" OH TYR A 418 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP B 393 " pdb=" OH TYR B 418 " model vdw 2.316 3.040 nonbonded pdb=" OD1 ASN A 349 " pdb=" OG SER A 394 " model vdw 2.325 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OE1 GLN B 488 " model vdw 2.328 3.040 ... (remaining 39246 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.130 Find NCS groups from input model: 0.160 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.005 0.061 5370 Z= 0.243 Angle : 1.079 9.916 7304 Z= 0.573 Chirality : 0.060 0.284 764 Planarity : 0.008 0.075 958 Dihedral : 13.455 81.821 1902 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.36 % Favored : 90.88 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.30), residues: 658 helix: -4.59 (0.25), residues: 45 sheet: -0.06 (0.41), residues: 178 loop : -2.47 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 36 HIS 0.006 0.001 HIS A 500 PHE 0.027 0.002 PHE A 451 TYR 0.046 0.003 TYR D 117 ARG 0.011 0.002 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.23994 ( 127) hydrogen bonds : angle 9.03998 ( 309) SS BOND : bond 0.00840 ( 12) SS BOND : angle 2.13116 ( 24) covalent geometry : bond 0.00500 ( 5358) covalent geometry : angle 1.07343 ( 7280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7620 (mmt90) REVERT: B 461 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.7738 (ttp-110) REVERT: E 18 LEU cc_start: 0.9125 (mm) cc_final: 0.8916 (mp) REVERT: E 44 GLU cc_start: 0.9066 (mp0) cc_final: 0.8639 (mp0) REVERT: E 87 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9104 (mttp) REVERT: A 381 LYS cc_start: 0.9487 (mppt) cc_final: 0.9264 (mmtm) REVERT: A 415 ASP cc_start: 0.8825 (t0) cc_final: 0.8592 (t0) REVERT: A 485 PHE cc_start: 0.7980 (m-80) cc_final: 0.7768 (m-10) REVERT: D 19 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8659 (mmm-85) REVERT: D 64 VAL cc_start: 0.9590 (m) cc_final: 0.9294 (m) REVERT: D 68 PHE cc_start: 0.9018 (m-10) cc_final: 0.8745 (m-10) REVERT: D 117 TYR cc_start: 0.7694 (t80) cc_final: 0.7357 (t80) REVERT: D 121 GLN cc_start: 0.8558 (pm20) cc_final: 0.8179 (pm20) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2178 time to fit residues: 46.3083 Evaluate side-chains 148 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN B 417 ASN B 488 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.108557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085944 restraints weight = 13058.498| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 6.49 r_work: 0.3088 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5370 Z= 0.123 Angle : 0.698 7.120 7304 Z= 0.357 Chirality : 0.047 0.154 764 Planarity : 0.005 0.067 958 Dihedral : 5.424 20.234 746 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.14 % Favored : 92.10 % Rotamer: Outliers : 2.50 % Allowed : 12.68 % Favored : 84.82 % 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 (0.31), residues: 658 helix: -4.19 (0.33), residues: 54 sheet: 0.24 (0.41), residues: 180 loop : -2.16 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 431 HIS 0.004 0.001 HIS A 500 PHE 0.035 0.001 PHE A 451 TYR 0.024 0.001 TYR D 117 ARG 0.006 0.001 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 127) hydrogen bonds : angle 6.48395 ( 309) SS BOND : bond 0.00456 ( 12) SS BOND : angle 1.15522 ( 24) covalent geometry : bond 0.00279 ( 5358) covalent geometry : angle 0.69553 ( 7280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8842 (mt-10) REVERT: B 412 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8607 (t0) REVERT: B 447 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8478 (mtm-85) REVERT: B 495 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.8999 (t) REVERT: E 5 GLN cc_start: 0.9274 (tp-100) cc_final: 0.9038 (tp-100) REVERT: E 87 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8778 (mttp) REVERT: A 341 ARG cc_start: 0.9338 (tmm-80) cc_final: 0.9130 (ttp80) REVERT: A 366 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 409 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8233 (mp10) REVERT: A 476 ASN cc_start: 0.8731 (m-40) cc_final: 0.7691 (p0) REVERT: A 485 PHE cc_start: 0.8133 (m-80) cc_final: 0.7863 (m-10) REVERT: D 59 TYR cc_start: 0.7853 (m-80) cc_final: 0.7455 (m-80) REVERT: D 77 ASN cc_start: 0.8712 (t0) cc_final: 0.8375 (t0) REVERT: D 117 TYR cc_start: 0.7596 (t80) cc_final: 0.7328 (t80) outliers start: 14 outliers final: 8 residues processed: 158 average time/residue: 0.2186 time to fit residues: 42.0054 Evaluate side-chains 151 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 76 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 51 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.3022 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085587 restraints weight = 13048.246| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 6.12 r_work: 0.3078 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5370 Z= 0.120 Angle : 0.665 7.559 7304 Z= 0.338 Chirality : 0.045 0.142 764 Planarity : 0.005 0.066 958 Dihedral : 4.999 18.190 746 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.14 % Favored : 92.25 % Rotamer: Outliers : 3.04 % Allowed : 16.25 % Favored : 80.71 % 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: -2.20 (0.31), residues: 658 helix: -3.84 (0.44), residues: 53 sheet: 0.23 (0.40), residues: 180 loop : -2.03 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.003 0.001 HIS A 500 PHE 0.028 0.001 PHE A 451 TYR 0.025 0.001 TYR E 111 ARG 0.005 0.001 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 127) hydrogen bonds : angle 6.12490 ( 309) SS BOND : bond 0.00427 ( 12) SS BOND : angle 0.97421 ( 24) covalent geometry : bond 0.00278 ( 5358) covalent geometry : angle 0.66372 ( 7280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8581 (pt0) REVERT: B 413 ILE cc_start: 0.9465 (mm) cc_final: 0.9249 (mm) REVERT: B 447 ARG cc_start: 0.8932 (mtp85) cc_final: 0.8557 (mtm-85) REVERT: B 495 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9031 (t) REVERT: E 5 GLN cc_start: 0.9323 (tp-100) cc_final: 0.9026 (tp-100) REVERT: E 76 LYS cc_start: 0.9126 (mttp) cc_final: 0.8892 (mtmm) REVERT: A 341 ARG cc_start: 0.9321 (tmm-80) cc_final: 0.9112 (ttp80) REVERT: A 366 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: A 409 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8190 (mp10) REVERT: A 485 PHE cc_start: 0.8169 (m-80) cc_final: 0.7865 (m-10) REVERT: D 19 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8517 (mmm-85) REVERT: D 59 TYR cc_start: 0.7844 (m-80) cc_final: 0.7480 (m-80) REVERT: D 74 ASN cc_start: 0.9644 (m-40) cc_final: 0.9370 (m-40) REVERT: D 77 ASN cc_start: 0.8764 (t0) cc_final: 0.8352 (t0) REVERT: D 103 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8319 (p) REVERT: D 117 TYR cc_start: 0.7936 (t80) cc_final: 0.7723 (t80) outliers start: 17 outliers final: 11 residues processed: 159 average time/residue: 0.2042 time to fit residues: 39.7492 Evaluate side-chains 152 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 0.0050 chunk 42 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.107696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084632 restraints weight = 13401.354| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 6.39 r_work: 0.3064 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5370 Z= 0.119 Angle : 0.673 8.074 7304 Z= 0.338 Chirality : 0.045 0.145 764 Planarity : 0.005 0.066 958 Dihedral : 4.785 17.621 746 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.14 % Favored : 92.40 % Rotamer: Outliers : 3.04 % Allowed : 18.75 % Favored : 78.21 % 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: -2.00 (0.31), residues: 658 helix: -3.99 (0.46), residues: 47 sheet: 0.52 (0.41), residues: 166 loop : -1.89 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.004 0.001 HIS A 500 PHE 0.021 0.001 PHE A 451 TYR 0.027 0.001 TYR D 118 ARG 0.007 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 127) hydrogen bonds : angle 5.76564 ( 309) SS BOND : bond 0.00386 ( 12) SS BOND : angle 0.95256 ( 24) covalent geometry : bond 0.00278 ( 5358) covalent geometry : angle 0.67201 ( 7280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9433 (ptt90) cc_final: 0.9210 (ptm-80) REVERT: B 401 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8622 (pt0) REVERT: B 495 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9052 (t) REVERT: E 5 GLN cc_start: 0.9357 (tp-100) cc_final: 0.9031 (tp-100) REVERT: E 87 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8573 (mttp) REVERT: E 113 ASP cc_start: 0.8277 (t0) cc_final: 0.8020 (t0) REVERT: A 341 ARG cc_start: 0.9345 (tmm-80) cc_final: 0.8941 (ttp80) REVERT: A 359 ASP cc_start: 0.8820 (p0) cc_final: 0.8583 (p0) REVERT: A 366 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: A 401 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8634 (mt-10) REVERT: A 485 PHE cc_start: 0.8200 (m-80) cc_final: 0.7887 (m-10) REVERT: D 74 ASN cc_start: 0.9646 (m-40) cc_final: 0.9397 (m-40) REVERT: D 77 ASN cc_start: 0.8577 (t0) cc_final: 0.8013 (t0) REVERT: D 103 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8258 (p) REVERT: D 117 TYR cc_start: 0.8074 (t80) cc_final: 0.7444 (t80) outliers start: 17 outliers final: 8 residues processed: 161 average time/residue: 0.2247 time to fit residues: 44.1270 Evaluate side-chains 146 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.0030 chunk 14 optimal weight: 0.7980 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN D 105 HIS 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 = 0.106879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083667 restraints weight = 13270.891| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 6.27 r_work: 0.3047 rms_B_bonded: 5.69 restraints_weight: 2.0000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5370 Z= 0.130 Angle : 0.676 8.517 7304 Z= 0.341 Chirality : 0.045 0.139 764 Planarity : 0.005 0.063 958 Dihedral : 4.655 17.816 746 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.60 % Favored : 91.95 % Rotamer: Outliers : 2.68 % Allowed : 19.64 % Favored : 77.68 % 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: -1.88 (0.31), residues: 658 helix: -3.80 (0.46), residues: 53 sheet: 0.51 (0.41), residues: 166 loop : -1.74 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 431 HIS 0.004 0.001 HIS A 500 PHE 0.016 0.001 PHE A 451 TYR 0.027 0.001 TYR E 111 ARG 0.007 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.02755 ( 127) hydrogen bonds : angle 5.62995 ( 309) SS BOND : bond 0.00366 ( 12) SS BOND : angle 0.95152 ( 24) covalent geometry : bond 0.00307 ( 5358) covalent geometry : angle 0.67487 ( 7280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9425 (ptt90) cc_final: 0.9213 (ptm-80) REVERT: B 401 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8612 (pt0) REVERT: E 5 GLN cc_start: 0.9393 (tp-100) cc_final: 0.9051 (tp-100) REVERT: E 38 ARG cc_start: 0.8954 (ptt180) cc_final: 0.8457 (ptm-80) REVERT: E 87 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8573 (mttp) REVERT: E 113 ASP cc_start: 0.8285 (t0) cc_final: 0.8004 (t0) REVERT: A 341 ARG cc_start: 0.9375 (tmm-80) cc_final: 0.8974 (ttp80) REVERT: A 359 ASP cc_start: 0.8869 (p0) cc_final: 0.8614 (p0) REVERT: A 366 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: D 77 ASN cc_start: 0.8783 (t0) cc_final: 0.8371 (t0) outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 0.2134 time to fit residues: 39.7270 Evaluate side-chains 144 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 GLN A 326 ASN A 409 GLN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081706 restraints weight = 13268.000| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 6.05 r_work: 0.3025 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5370 Z= 0.148 Angle : 0.700 8.557 7304 Z= 0.354 Chirality : 0.045 0.137 764 Planarity : 0.005 0.062 958 Dihedral : 4.728 19.520 746 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.90 % Favored : 91.64 % Rotamer: Outliers : 2.68 % Allowed : 21.07 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.32), residues: 658 helix: -3.71 (0.51), residues: 47 sheet: 0.37 (0.40), residues: 176 loop : -1.68 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.005 0.001 HIS A 500 PHE 0.014 0.001 PHE A 451 TYR 0.029 0.001 TYR E 111 ARG 0.007 0.001 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 127) hydrogen bonds : angle 5.61092 ( 309) SS BOND : bond 0.00459 ( 12) SS BOND : angle 1.04105 ( 24) covalent geometry : bond 0.00348 ( 5358) covalent geometry : angle 0.69867 ( 7280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9403 (ptt90) cc_final: 0.9187 (ptm-80) REVERT: B 401 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8557 (mt-10) REVERT: E 5 GLN cc_start: 0.9419 (tp-100) cc_final: 0.9048 (tp-100) REVERT: E 38 ARG cc_start: 0.8961 (ptt180) cc_final: 0.8514 (ptm-80) REVERT: E 87 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8551 (mttp) REVERT: E 113 ASP cc_start: 0.8295 (t0) cc_final: 0.7991 (t0) REVERT: A 341 ARG cc_start: 0.9381 (tmm-80) cc_final: 0.9012 (ttp80) REVERT: A 366 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: D 77 ASN cc_start: 0.8850 (t0) cc_final: 0.8530 (t0) REVERT: D 80 TYR cc_start: 0.8462 (m-80) cc_final: 0.8258 (m-80) outliers start: 15 outliers final: 11 residues processed: 145 average time/residue: 0.2216 time to fit residues: 39.3662 Evaluate side-chains 144 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 76 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.0000 chunk 42 optimal weight: 0.0170 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081526 restraints weight = 13169.415| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 6.16 r_work: 0.3023 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5370 Z= 0.146 Angle : 0.722 9.114 7304 Z= 0.364 Chirality : 0.045 0.149 764 Planarity : 0.005 0.062 958 Dihedral : 4.729 19.169 746 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.75 % Favored : 91.79 % Rotamer: Outliers : 2.32 % Allowed : 23.04 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.31), residues: 658 helix: -3.88 (0.44), residues: 53 sheet: 0.37 (0.40), residues: 176 loop : -1.63 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.004 0.001 HIS A 500 PHE 0.013 0.001 PHE A 451 TYR 0.029 0.001 TYR E 111 ARG 0.007 0.001 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.02748 ( 127) hydrogen bonds : angle 5.63617 ( 309) SS BOND : bond 0.00461 ( 12) SS BOND : angle 1.20675 ( 24) covalent geometry : bond 0.00347 ( 5358) covalent geometry : angle 0.71953 ( 7280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9397 (ptt90) cc_final: 0.9179 (ptm-80) REVERT: B 381 LYS cc_start: 0.4296 (tttt) cc_final: 0.4014 (tttt) REVERT: B 401 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8539 (mt-10) REVERT: E 5 GLN cc_start: 0.9443 (tp-100) cc_final: 0.9049 (tp-100) REVERT: E 38 ARG cc_start: 0.8960 (ptt180) cc_final: 0.8519 (ptm-80) REVERT: E 87 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8600 (mttp) REVERT: E 113 ASP cc_start: 0.8274 (t0) cc_final: 0.7957 (t0) REVERT: A 341 ARG cc_start: 0.9379 (tmm-80) cc_final: 0.9005 (ttp80) REVERT: A 366 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: D 77 ASN cc_start: 0.8823 (t0) cc_final: 0.8557 (t0) outliers start: 13 outliers final: 9 residues processed: 147 average time/residue: 0.2343 time to fit residues: 42.0740 Evaluate side-chains 140 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain D residue 76 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 GLN E 32 HIS ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075168 restraints weight = 13616.421| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 6.47 r_work: 0.2906 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 5370 Z= 0.291 Angle : 0.840 10.106 7304 Z= 0.435 Chirality : 0.049 0.173 764 Planarity : 0.006 0.060 958 Dihedral : 5.447 23.487 746 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.03 % Favored : 89.51 % Rotamer: Outliers : 2.68 % Allowed : 23.57 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.32), residues: 658 helix: -4.12 (0.42), residues: 42 sheet: -0.03 (0.37), residues: 200 loop : -1.62 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 36 HIS 0.007 0.002 HIS D 30 PHE 0.016 0.002 PHE A 324 TYR 0.037 0.002 TYR E 111 ARG 0.007 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 127) hydrogen bonds : angle 5.82197 ( 309) SS BOND : bond 0.00648 ( 12) SS BOND : angle 1.47152 ( 24) covalent geometry : bond 0.00675 ( 5358) covalent geometry : angle 0.83688 ( 7280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9452 (ptt90) cc_final: 0.9235 (ptm-80) REVERT: E 5 GLN cc_start: 0.9479 (tp-100) cc_final: 0.9157 (tp-100) REVERT: E 87 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8580 (mttp) REVERT: A 366 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: A 427 CYS cc_start: 0.8562 (m) cc_final: 0.8353 (m) REVERT: D 19 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8581 (mmm-85) REVERT: D 77 ASN cc_start: 0.9031 (t0) cc_final: 0.8811 (t0) REVERT: D 99 ASP cc_start: 0.8510 (t0) cc_final: 0.8057 (t0) outliers start: 15 outliers final: 9 residues processed: 140 average time/residue: 0.2094 time to fit residues: 36.2443 Evaluate side-chains 135 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain D residue 76 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077912 restraints weight = 13451.616| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 6.37 r_work: 0.2964 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5370 Z= 0.160 Angle : 0.800 10.171 7304 Z= 0.406 Chirality : 0.047 0.153 764 Planarity : 0.005 0.063 958 Dihedral : 5.079 22.129 746 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.05 % Favored : 91.49 % Rotamer: Outliers : 2.14 % Allowed : 24.82 % Favored : 73.04 % 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: -1.85 (0.32), residues: 658 helix: -3.80 (0.47), residues: 48 sheet: -0.03 (0.38), residues: 190 loop : -1.56 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.006 0.002 HIS A 514 PHE 0.013 0.001 PHE A 451 TYR 0.033 0.001 TYR E 111 ARG 0.008 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 127) hydrogen bonds : angle 5.83752 ( 309) SS BOND : bond 0.00525 ( 12) SS BOND : angle 1.16048 ( 24) covalent geometry : bond 0.00384 ( 5358) covalent geometry : angle 0.79824 ( 7280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9431 (ptt90) cc_final: 0.9214 (ptm-80) REVERT: B 401 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8731 (mt-10) REVERT: E 5 GLN cc_start: 0.9476 (tp-100) cc_final: 0.9145 (tp-100) REVERT: E 87 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8463 (mttp) REVERT: A 366 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: A 377 VAL cc_start: 0.9172 (m) cc_final: 0.8930 (m) REVERT: D 55 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.9059 (p0) REVERT: D 77 ASN cc_start: 0.8901 (t0) cc_final: 0.8637 (t0) REVERT: D 84 ASN cc_start: 0.9379 (m-40) cc_final: 0.9145 (m-40) outliers start: 12 outliers final: 7 residues processed: 142 average time/residue: 0.2076 time to fit residues: 36.3226 Evaluate side-chains 142 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 76 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077191 restraints weight = 13483.899| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 6.49 r_work: 0.2959 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5370 Z= 0.181 Angle : 0.817 10.041 7304 Z= 0.414 Chirality : 0.047 0.146 764 Planarity : 0.005 0.062 958 Dihedral : 5.051 20.593 746 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 1.79 % Allowed : 24.82 % Favored : 73.39 % 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: -1.91 (0.32), residues: 658 helix: -3.65 (0.44), residues: 60 sheet: 0.06 (0.39), residues: 180 loop : -1.58 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.006 0.002 HIS D 30 PHE 0.013 0.001 PHE A 451 TYR 0.032 0.001 TYR E 111 ARG 0.008 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 127) hydrogen bonds : angle 5.75957 ( 309) SS BOND : bond 0.00503 ( 12) SS BOND : angle 1.22368 ( 24) covalent geometry : bond 0.00434 ( 5358) covalent geometry : angle 0.81522 ( 7280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9424 (ptt90) cc_final: 0.9207 (ptm-80) REVERT: E 5 GLN cc_start: 0.9479 (tp-100) cc_final: 0.9160 (tp-100) REVERT: E 87 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8510 (mttp) REVERT: A 366 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: A 460 GLU cc_start: 0.8845 (tp30) cc_final: 0.8632 (tp30) REVERT: D 77 ASN cc_start: 0.8893 (t0) cc_final: 0.8686 (t0) outliers start: 10 outliers final: 9 residues processed: 135 average time/residue: 0.2107 time to fit residues: 35.1357 Evaluate side-chains 136 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain D residue 76 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078621 restraints weight = 13586.359| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 6.12 r_work: 0.2949 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5370 Z= 0.199 Angle : 0.836 10.576 7304 Z= 0.424 Chirality : 0.047 0.148 764 Planarity : 0.006 0.061 958 Dihedral : 5.114 19.738 746 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 2.14 % Allowed : 25.36 % Favored : 72.50 % 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: -1.86 (0.32), residues: 658 helix: -3.61 (0.47), residues: 54 sheet: 0.13 (0.40), residues: 178 loop : -1.60 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.007 0.002 HIS D 30 PHE 0.012 0.001 PHE A 451 TYR 0.033 0.001 TYR E 111 ARG 0.010 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 127) hydrogen bonds : angle 5.72813 ( 309) SS BOND : bond 0.00541 ( 12) SS BOND : angle 1.22275 ( 24) covalent geometry : bond 0.00473 ( 5358) covalent geometry : angle 0.83411 ( 7280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.17 seconds wall clock time: 67 minutes 28.43 seconds (4048.43 seconds total)