Starting phenix.real_space_refine on Thu Jun 5 05:27:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co7_45772/06_2025/9co7_45772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co7_45772/06_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_45772/06_2025/9co7_45772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co7_45772/06_2025/9co7_45772.map" model { file = "/net/cci-nas-00/data/ceres_data/9co7_45772/06_2025/9co7_45772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co7_45772/06_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-5710/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: 4.15, per 1000 atoms: 0.80 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: 1.25 Conformation dependent library (CDL) restraints added in 684.9 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: 0.67 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: 1.50 Time building geometry restraints manager: 1.50 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: 3.220 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.970 ------------------------------------------------------------------------------- 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 : 0.569 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: 0.2206 time to fit residues: 46.6788 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 : 0.627 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.108053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085330 restraints weight = 13069.352| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 6.44 r_work: 0.3078 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1913 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= 0.125 Angle : 0.695 6.947 7304 Z= 0.356 Chirality : 0.047 0.150 764 Planarity : 0.005 0.067 958 Dihedral : 5.405 20.019 746 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % Rotamer: Outliers : 2.50 % Allowed : 12.86 % Favored : 84.64 % 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: -2.35 (0.31), residues: 658 helix: -4.19 (0.33), residues: 54 sheet: 0.24 (0.41), residues: 180 loop : -2.15 (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 0.034 0.001 PHE A 451 TYR 0.023 0.001 TYR D 117 ARG 0.006 0.001 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 127) hydrogen bonds : angle 6.42565 ( 309) SS BOND : bond 0.00456 ( 12) SS BOND : angle 1.15325 ( 24) covalent geometry : bond 0.00285 ( 5358) covalent geometry : angle 0.69274 ( 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 : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8831 (mt-10) REVERT: B 412 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8629 (t0) REVERT: B 447 ARG cc_start: 0.8947 (mtp85) cc_final: 0.8491 (mtm-85) REVERT: B 466 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8444 (mm-30) REVERT: B 495 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9016 (t) REVERT: E 5 GLN cc_start: 0.9284 (tp-100) cc_final: 0.9051 (tp-100) REVERT: E 87 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8531 (mttm) REVERT: A 341 ARG cc_start: 0.9325 (tmm-80) cc_final: 0.9118 (ttp80) REVERT: A 366 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: A 409 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8233 (mp10) REVERT: A 461 ARG cc_start: 0.9134 (ttm170) cc_final: 0.8920 (ttm110) REVERT: A 476 ASN cc_start: 0.8741 (m-40) cc_final: 0.7696 (p0) REVERT: A 485 PHE cc_start: 0.8177 (m-80) cc_final: 0.7892 (m-10) REVERT: D 59 TYR cc_start: 0.7864 (m-80) cc_final: 0.7463 (m-80) REVERT: D 77 ASN cc_start: 0.8746 (t0) cc_final: 0.8418 (t0) REVERT: D 117 TYR cc_start: 0.7533 (t80) cc_final: 0.7298 (t80) outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 0.2214 time to fit residues: 42.4598 Evaluate side-chains 150 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** 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 = 0.3720 r_free = 0.3720 target = 0.106456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083501 restraints weight = 13020.128| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 6.20 r_work: 0.3041 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2408 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= 0.139 Angle : 0.677 7.550 7304 Z= 0.345 Chirality : 0.046 0.154 764 Planarity : 0.005 0.066 958 Dihedral : 5.116 18.897 746 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.45 % Favored : 91.95 % Rotamer: Outliers : 2.86 % Allowed : 16.96 % Favored : 80.18 % 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: -2.17 (0.31), residues: 658 helix: -3.87 (0.48), residues: 47 sheet: 0.33 (0.41), residues: 176 loop : -2.06 (0.27), residues: 435 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 0.027 0.001 PHE A 451 TYR 0.025 0.001 TYR E 111 ARG 0.004 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 127) hydrogen bonds : angle 6.12643 ( 309) SS BOND : bond 0.00437 ( 12) SS BOND : angle 1.00509 ( 24) covalent geometry : bond 0.00323 ( 5358) covalent geometry : angle 0.67517 ( 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 162 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9451 (ptt90) cc_final: 0.9228 (ptm-80) REVERT: B 381 LYS cc_start: 0.4452 (tttt) cc_final: 0.4170 (tttt) REVERT: B 401 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8660 (pt0) REVERT: B 447 ARG cc_start: 0.9000 (mtp85) cc_final: 0.8623 (mtm-85) REVERT: B 495 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9034 (t) REVERT: E 5 GLN cc_start: 0.9355 (tp-100) cc_final: 0.9055 (tp-100) REVERT: A 341 ARG cc_start: 0.9329 (tmm-80) cc_final: 0.9126 (ttp80) REVERT: A 366 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: A 452 ARG cc_start: 0.9227 (ttp80) cc_final: 0.8301 (ttp80) REVERT: A 485 PHE cc_start: 0.8311 (m-80) cc_final: 0.7975 (m-10) REVERT: D 59 TYR cc_start: 0.7947 (m-80) cc_final: 0.7557 (m-80) REVERT: D 74 ASN cc_start: 0.9628 (m-40) cc_final: 0.9337 (m-40) REVERT: D 77 ASN cc_start: 0.8826 (t0) cc_final: 0.8426 (t0) REVERT: D 103 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8301 (p) outliers start: 16 outliers final: 11 residues processed: 154 average time/residue: 0.2123 time to fit residues: 40.0841 Evaluate side-chains 144 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN D 77 ASN ** D 105 HIS ** 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 = 0.3724 r_free = 0.3724 target = 0.106601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083469 restraints weight = 13398.739| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 6.29 r_work: 0.3043 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2784 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= 0.127 Angle : 0.683 8.178 7304 Z= 0.344 Chirality : 0.045 0.137 764 Planarity : 0.005 0.066 958 Dihedral : 4.896 18.823 746 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.99 % Favored : 92.55 % Rotamer: Outliers : 3.21 % Allowed : 18.21 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.31), residues: 658 helix: -4.09 (0.44), residues: 47 sheet: 0.50 (0.41), residues: 166 loop : -1.85 (0.27), residues: 445 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 0.020 0.001 PHE A 451 TYR 0.026 0.001 TYR E 111 ARG 0.006 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 127) hydrogen bonds : angle 5.81185 ( 309) SS BOND : bond 0.00424 ( 12) SS BOND : angle 1.00063 ( 24) covalent geometry : bond 0.00298 ( 5358) covalent geometry : angle 0.68213 ( 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 163 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9436 (ptt90) cc_final: 0.9210 (ptm-80) REVERT: B 401 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8663 (pt0) REVERT: B 495 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9059 (t) REVERT: E 5 GLN cc_start: 0.9389 (tp-100) cc_final: 0.9058 (tp-100) REVERT: E 87 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8549 (mttp) REVERT: E 113 ASP cc_start: 0.8324 (t0) cc_final: 0.8050 (t0) REVERT: A 341 ARG cc_start: 0.9357 (tmm-80) cc_final: 0.8924 (ttp80) REVERT: A 359 ASP cc_start: 0.8849 (p0) cc_final: 0.8593 (p0) REVERT: A 366 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: D 59 TYR cc_start: 0.7856 (m-80) cc_final: 0.7626 (m-80) REVERT: D 77 ASN cc_start: 0.8636 (t0) cc_final: 0.8091 (t0) REVERT: D 80 TYR cc_start: 0.8151 (m-10) cc_final: 0.7917 (m-80) REVERT: D 103 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8305 (p) REVERT: D 117 TYR cc_start: 0.7844 (t80) cc_final: 0.7279 (t80) outliers start: 18 outliers final: 9 residues processed: 155 average time/residue: 0.2394 time to fit residues: 44.8116 Evaluate side-chains 148 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 328 THR 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: 2.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.103384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079698 restraints weight = 13357.234| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 6.01 r_work: 0.2987 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5370 Z= 0.190 Angle : 0.709 8.490 7304 Z= 0.359 Chirality : 0.046 0.142 764 Planarity : 0.005 0.061 958 Dihedral : 5.028 21.237 746 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % Rotamer: Outliers : 3.04 % Allowed : 19.82 % Favored : 77.14 % 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: -1.90 (0.31), residues: 658 helix: -4.22 (0.44), residues: 41 sheet: 0.33 (0.40), residues: 176 loop : -1.75 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.005 0.001 HIS A 500 PHE 0.016 0.001 PHE A 451 TYR 0.029 0.002 TYR E 111 ARG 0.007 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 127) hydrogen bonds : angle 5.66679 ( 309) SS BOND : bond 0.00419 ( 12) SS BOND : angle 1.10383 ( 24) covalent geometry : bond 0.00439 ( 5358) covalent geometry : angle 0.70731 ( 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 149 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9439 (ptt90) cc_final: 0.9215 (ptm-80) REVERT: B 401 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8556 (mt-10) REVERT: E 5 GLN cc_start: 0.9436 (tp-100) cc_final: 0.9056 (tp-100) REVERT: E 87 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8582 (mttp) REVERT: A 359 ASP cc_start: 0.8931 (p0) cc_final: 0.8600 (p0) REVERT: A 366 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: A 401 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8578 (tt0) REVERT: D 59 TYR cc_start: 0.8087 (m-80) cc_final: 0.7692 (m-80) REVERT: D 77 ASN cc_start: 0.8874 (t0) cc_final: 0.8482 (t0) REVERT: D 80 TYR cc_start: 0.8275 (m-10) cc_final: 0.7955 (m-80) outliers start: 17 outliers final: 11 residues processed: 142 average time/residue: 0.2122 time to fit residues: 37.0644 Evaluate side-chains 141 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 374 CYS 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 76 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 GLN A 326 ASN ** D 5 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.102688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079274 restraints weight = 13416.102| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 5.92 r_work: 0.2982 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5370 Z= 0.175 Angle : 0.720 9.045 7304 Z= 0.364 Chirality : 0.046 0.137 764 Planarity : 0.005 0.062 958 Dihedral : 4.999 22.593 746 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.60 % Favored : 91.95 % Rotamer: Outliers : 3.21 % Allowed : 20.71 % Favored : 76.07 % 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 (0.31), residues: 658 helix: -4.21 (0.41), residues: 47 sheet: 0.35 (0.39), residues: 176 loop : -1.66 (0.28), residues: 435 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 0.015 0.001 PHE A 451 TYR 0.030 0.001 TYR E 111 ARG 0.006 0.001 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 127) hydrogen bonds : angle 5.74447 ( 309) SS BOND : bond 0.00495 ( 12) SS BOND : angle 1.11415 ( 24) covalent geometry : bond 0.00410 ( 5358) covalent geometry : angle 0.71862 ( 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 157 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9430 (ptt90) cc_final: 0.9219 (ptm-80) REVERT: B 401 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8539 (mt-10) REVERT: E 5 GLN cc_start: 0.9426 (tp-100) cc_final: 0.9099 (tp-100) REVERT: E 87 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8574 (mttp) REVERT: A 359 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8618 (p0) REVERT: A 366 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: A 401 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8335 (tt0) REVERT: D 19 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.7906 (mmm-85) REVERT: D 59 TYR cc_start: 0.8081 (m-80) cc_final: 0.7659 (m-80) REVERT: D 77 ASN cc_start: 0.8950 (t0) cc_final: 0.8579 (t0) REVERT: D 80 TYR cc_start: 0.8321 (m-10) cc_final: 0.7881 (m-80) outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.2274 time to fit residues: 41.1483 Evaluate side-chains 141 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 359 ASP 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 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: 0.7980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 54 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 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 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 = 0.3670 r_free = 0.3670 target = 0.102872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079599 restraints weight = 13211.138| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 5.84 r_work: 0.2996 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3629 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= 0.156 Angle : 0.732 9.612 7304 Z= 0.369 Chirality : 0.045 0.135 764 Planarity : 0.005 0.062 958 Dihedral : 4.888 22.137 746 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.36 % Favored : 91.19 % Rotamer: Outliers : 2.32 % Allowed : 22.14 % Favored : 75.54 % 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: -4.23 (0.39), residues: 48 sheet: 0.50 (0.40), residues: 166 loop : -1.64 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 431 HIS 0.004 0.001 HIS D 30 PHE 0.014 0.001 PHE A 451 TYR 0.031 0.001 TYR E 111 ARG 0.007 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 127) hydrogen bonds : angle 5.67277 ( 309) SS BOND : bond 0.00485 ( 12) SS BOND : angle 1.27010 ( 24) covalent geometry : bond 0.00372 ( 5358) covalent geometry : angle 0.72936 ( 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 148 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 335 GLU cc_start: 0.9271 (mp0) cc_final: 0.9071 (mp0) REVERT: B 341 ARG cc_start: 0.9416 (ptt90) cc_final: 0.9204 (ptm-80) REVERT: B 401 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8522 (mt-10) REVERT: E 5 GLN cc_start: 0.9443 (tp-100) cc_final: 0.9113 (tp-100) REVERT: E 87 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8535 (mttp) REVERT: A 366 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: A 401 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8404 (tt0) REVERT: D 55 ASP cc_start: 0.9290 (m-30) cc_final: 0.9036 (p0) REVERT: D 59 TYR cc_start: 0.7983 (m-80) cc_final: 0.7579 (m-80) REVERT: D 77 ASN cc_start: 0.8902 (t0) cc_final: 0.8563 (t0) REVERT: D 80 TYR cc_start: 0.8371 (m-10) cc_final: 0.7959 (m-80) outliers start: 13 outliers final: 9 residues processed: 141 average time/residue: 0.2203 time to fit residues: 38.7036 Evaluate side-chains 138 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3673 r_free = 0.3673 target = 0.103007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079787 restraints weight = 13441.308| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 5.94 r_work: 0.2997 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5370 Z= 0.153 Angle : 0.754 9.230 7304 Z= 0.380 Chirality : 0.046 0.148 764 Planarity : 0.005 0.062 958 Dihedral : 4.826 22.470 746 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.29 % Favored : 92.25 % Rotamer: Outliers : 2.32 % Allowed : 23.39 % Favored : 74.29 % 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: -1.81 (0.32), residues: 658 helix: -4.14 (0.42), residues: 48 sheet: 0.31 (0.39), residues: 176 loop : -1.59 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.005 0.002 HIS E 30 PHE 0.012 0.001 PHE A 451 TYR 0.031 0.001 TYR E 111 ARG 0.008 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 127) hydrogen bonds : angle 5.68782 ( 309) SS BOND : bond 0.00572 ( 12) SS BOND : angle 1.26034 ( 24) covalent geometry : bond 0.00367 ( 5358) covalent geometry : angle 0.75130 ( 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 146 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9422 (ptt90) cc_final: 0.9212 (ptm-80) REVERT: B 401 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8519 (mt-10) REVERT: E 5 GLN cc_start: 0.9458 (tp-100) cc_final: 0.9118 (tp-100) REVERT: E 38 ARG cc_start: 0.9008 (ptt180) cc_final: 0.8539 (ptm-80) REVERT: E 87 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8498 (mttp) REVERT: A 366 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: A 381 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9121 (ptmm) REVERT: A 461 ARG cc_start: 0.9051 (ttm170) cc_final: 0.8623 (ttm110) REVERT: D 6 GLU cc_start: 0.8682 (mp0) cc_final: 0.7870 (mp0) REVERT: D 59 TYR cc_start: 0.7992 (m-80) cc_final: 0.7643 (m-80) REVERT: D 77 ASN cc_start: 0.8862 (t0) cc_final: 0.8558 (t0) REVERT: D 80 TYR cc_start: 0.8374 (m-10) cc_final: 0.7961 (m-80) outliers start: 13 outliers final: 10 residues processed: 139 average time/residue: 0.2229 time to fit residues: 37.7472 Evaluate side-chains 140 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 B residue 519 VAL 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 64 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.101912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076982 restraints weight = 13473.519| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 6.64 r_work: 0.2953 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5370 Z= 0.184 Angle : 0.790 9.832 7304 Z= 0.400 Chirality : 0.047 0.175 764 Planarity : 0.005 0.061 958 Dihedral : 4.961 22.407 746 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.81 % Favored : 90.73 % Rotamer: Outliers : 2.68 % Allowed : 23.75 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.32), residues: 658 helix: -4.16 (0.42), residues: 48 sheet: 0.51 (0.40), residues: 164 loop : -1.56 (0.29), residues: 446 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 0.033 0.001 TYR E 111 ARG 0.008 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 127) hydrogen bonds : angle 5.71182 ( 309) SS BOND : bond 0.00555 ( 12) SS BOND : angle 1.21890 ( 24) covalent geometry : bond 0.00436 ( 5358) covalent geometry : angle 0.78815 ( 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 144 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9465 (ptt90) cc_final: 0.9247 (ptm-80) REVERT: B 401 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8536 (mt-10) REVERT: E 5 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9144 (tp-100) REVERT: E 87 LYS cc_start: 0.8961 (mtmm) cc_final: 0.8522 (mttp) REVERT: A 366 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: A 460 GLU cc_start: 0.9039 (tp30) cc_final: 0.8739 (tp30) REVERT: A 461 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8022 (ttm110) REVERT: D 19 ARG cc_start: 0.9063 (mmm-85) cc_final: 0.8055 (mmm-85) REVERT: D 55 ASP cc_start: 0.9302 (m-30) cc_final: 0.9043 (p0) REVERT: D 59 TYR cc_start: 0.7964 (m-80) cc_final: 0.7605 (m-80) REVERT: D 77 ASN cc_start: 0.8999 (t0) cc_final: 0.8750 (t0) REVERT: D 80 TYR cc_start: 0.8331 (m-10) cc_final: 0.7870 (m-80) outliers start: 15 outliers final: 12 residues processed: 137 average time/residue: 0.2220 time to fit residues: 36.9373 Evaluate side-chains 140 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 A residue 387 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain D residue 48 VAL 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: 0.5980 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077729 restraints weight = 13508.461| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 6.60 r_work: 0.2977 rms_B_bonded: 5.70 restraints_weight: 2.0000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5370 Z= 0.157 Angle : 0.792 10.264 7304 Z= 0.399 Chirality : 0.046 0.150 764 Planarity : 0.005 0.062 958 Dihedral : 4.799 20.370 746 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.29 % Favored : 92.25 % Rotamer: Outliers : 2.50 % Allowed : 24.82 % Favored : 72.68 % 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: -1.70 (0.32), residues: 658 helix: -3.83 (0.46), residues: 54 sheet: 0.55 (0.41), residues: 164 loop : -1.52 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 431 HIS 0.005 0.001 HIS D 30 PHE 0.012 0.001 PHE A 451 TYR 0.032 0.001 TYR E 111 ARG 0.009 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 127) hydrogen bonds : angle 5.73000 ( 309) SS BOND : bond 0.00496 ( 12) SS BOND : angle 1.13206 ( 24) covalent geometry : bond 0.00379 ( 5358) covalent geometry : angle 0.79040 ( 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 149 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9446 (ptt90) cc_final: 0.9230 (ptm-80) REVERT: B 401 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8544 (mt-10) REVERT: E 5 GLN cc_start: 0.9464 (tp-100) cc_final: 0.9147 (tp-100) REVERT: E 87 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8473 (mttp) REVERT: A 341 ARG cc_start: 0.9282 (ttp80) cc_final: 0.9079 (tmm-80) REVERT: A 366 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 381 LYS cc_start: 0.9590 (mmmt) cc_final: 0.8855 (tptp) REVERT: A 460 GLU cc_start: 0.8997 (tp30) cc_final: 0.8644 (tp30) REVERT: A 461 ARG cc_start: 0.8862 (ttm170) cc_final: 0.8074 (ttm110) REVERT: A 495 THR cc_start: 0.9485 (p) cc_final: 0.9275 (p) REVERT: D 19 ARG cc_start: 0.9077 (mmm-85) cc_final: 0.8359 (mmm-85) REVERT: D 59 TYR cc_start: 0.7940 (m-80) cc_final: 0.7635 (m-80) REVERT: D 80 TYR cc_start: 0.8368 (m-10) cc_final: 0.8025 (m-80) outliers start: 14 outliers final: 11 residues processed: 141 average time/residue: 0.2199 time to fit residues: 37.8936 Evaluate side-chains 141 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 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 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain D residue 48 VAL 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: 6.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077505 restraints weight = 13558.458| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 6.51 r_work: 0.2965 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5370 Z= 0.173 Angle : 0.796 10.062 7304 Z= 0.403 Chirality : 0.046 0.154 764 Planarity : 0.005 0.062 958 Dihedral : 4.842 19.702 746 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % Rotamer: Outliers : 2.14 % Allowed : 25.71 % Favored : 72.14 % 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: -1.70 (0.32), residues: 658 helix: -3.83 (0.45), residues: 54 sheet: 0.58 (0.41), residues: 164 loop : -1.54 (0.29), residues: 440 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 0.032 0.001 TYR E 111 ARG 0.008 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 127) hydrogen bonds : angle 5.71883 ( 309) SS BOND : bond 0.00490 ( 12) SS BOND : angle 1.12150 ( 24) covalent geometry : bond 0.00415 ( 5358) covalent geometry : angle 0.79515 ( 7280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3899.37 seconds wall clock time: 67 minutes 27.68 seconds (4047.68 seconds total)