Starting phenix.real_space_refine on Wed Sep 17 05:34:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co7_45772/09_2025/9co7_45772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co7_45772/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9co7_45772/09_2025/9co7_45772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co7_45772/09_2025/9co7_45772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9co7_45772/09_2025/9co7_45772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co7_45772/09_2025/9co7_45772.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.30 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: 0.39 Conformation dependent library (CDL) restraints added in 213.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.19 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: 0.74 Time building geometry restraints manager: 0.51 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: 0.01 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.700 Find NCS groups from input model: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- 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 : 5.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (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 ARG 0.011 0.002 ARG B 449 TYR 0.046 0.003 TYR D 117 PHE 0.027 0.002 PHE A 451 TRP 0.033 0.002 TRP D 36 HIS 0.006 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 5358) covalent geometry : angle 1.07343 ( 7280) SS BOND : bond 0.00840 ( 12) SS BOND : angle 2.13116 ( 24) hydrogen bonds : bond 0.23994 ( 127) hydrogen bonds : angle 9.03998 ( 309) *********************** 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 : 0.224 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: 0.1016 time to fit residues: 21.6143 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081590 restraints weight = 13224.651| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 6.28 r_work: 0.2997 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2107 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= 0.182 Angle : 0.722 7.872 7304 Z= 0.373 Chirality : 0.048 0.154 764 Planarity : 0.006 0.065 958 Dihedral : 5.621 21.307 746 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.05 % Favored : 91.19 % Rotamer: Outliers : 2.68 % Allowed : 13.39 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.31), residues: 658 helix: -4.24 (0.41), residues: 41 sheet: 0.21 (0.41), residues: 180 loop : -2.18 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 341 TYR 0.023 0.002 TYR D 117 PHE 0.034 0.001 PHE A 451 TRP 0.013 0.001 TRP B 431 HIS 0.006 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 5358) covalent geometry : angle 0.71967 ( 7280) SS BOND : bond 0.00483 ( 12) SS BOND : angle 1.25597 ( 24) hydrogen bonds : bond 0.03650 ( 127) hydrogen bonds : angle 6.33353 ( 309) *********************** 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 164 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9473 (ptt90) cc_final: 0.9247 (ptm-80) REVERT: B 412 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8784 (t0) REVERT: E 5 GLN cc_start: 0.9332 (tp-100) cc_final: 0.9072 (tp-100) REVERT: E 46 GLU cc_start: 0.8146 (pm20) cc_final: 0.7936 (mp0) REVERT: A 341 ARG cc_start: 0.9341 (tmm-80) cc_final: 0.9136 (ttp80) REVERT: A 359 ASP cc_start: 0.8800 (p0) cc_final: 0.8579 (p0) REVERT: A 366 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: A 409 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8195 (mp10) REVERT: A 485 PHE cc_start: 0.8428 (m-80) cc_final: 0.8207 (m-10) REVERT: D 77 ASN cc_start: 0.8901 (t0) cc_final: 0.8617 (t0) REVERT: D 103 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8390 (p) outliers start: 15 outliers final: 7 residues processed: 157 average time/residue: 0.1011 time to fit residues: 19.3372 Evaluate side-chains 145 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 412 ASN 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 E residue 69 THR 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 103 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.103380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079870 restraints weight = 13312.472| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 6.06 r_work: 0.2987 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5370 Z= 0.179 Angle : 0.712 8.624 7304 Z= 0.362 Chirality : 0.046 0.156 764 Planarity : 0.005 0.064 958 Dihedral : 5.371 21.625 746 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % Rotamer: Outliers : 3.57 % Allowed : 17.68 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.31), residues: 658 helix: -3.85 (0.51), residues: 41 sheet: 0.35 (0.40), residues: 176 loop : -1.98 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 341 TYR 0.026 0.002 TYR E 111 PHE 0.026 0.001 PHE A 451 TRP 0.012 0.002 TRP B 431 HIS 0.005 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 5358) covalent geometry : angle 0.70987 ( 7280) SS BOND : bond 0.00481 ( 12) SS BOND : angle 1.12413 ( 24) hydrogen bonds : bond 0.03501 ( 127) hydrogen bonds : angle 6.04373 ( 309) *********************** 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 165 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9445 (ptt90) cc_final: 0.9231 (ptm-80) REVERT: B 401 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8741 (mt-10) REVERT: B 412 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8535 (t0) REVERT: E 5 GLN cc_start: 0.9397 (tp-100) cc_final: 0.9051 (tp-100) REVERT: E 6 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: E 87 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8578 (mttp) REVERT: A 341 ARG cc_start: 0.9357 (tmm-80) cc_final: 0.9142 (ttp80) REVERT: A 359 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8513 (p0) REVERT: A 366 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: A 485 PHE cc_start: 0.8480 (m-80) cc_final: 0.8216 (m-10) REVERT: D 76 LYS cc_start: 0.9473 (mttm) cc_final: 0.9243 (ptpp) REVERT: D 77 ASN cc_start: 0.8937 (t0) cc_final: 0.8571 (t0) REVERT: D 103 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (p) outliers start: 20 outliers final: 13 residues processed: 155 average time/residue: 0.0959 time to fit residues: 18.2494 Evaluate side-chains 153 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain E residue 6 GLU 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 E residue 69 THR Chi-restraints excluded: chain A residue 359 ASP 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 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN A 409 GLN D 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078718 restraints weight = 13296.279| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 6.64 r_work: 0.2971 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2988 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 : 0.695 8.035 7304 Z= 0.351 Chirality : 0.045 0.138 764 Planarity : 0.005 0.062 958 Dihedral : 5.154 22.668 746 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.05 % Favored : 91.49 % Rotamer: Outliers : 3.75 % Allowed : 19.29 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.31), residues: 658 helix: -3.87 (0.47), residues: 47 sheet: 0.55 (0.41), residues: 166 loop : -1.92 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 119 TYR 0.028 0.001 TYR E 111 PHE 0.020 0.001 PHE A 451 TRP 0.010 0.001 TRP B 431 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5358) covalent geometry : angle 0.69371 ( 7280) SS BOND : bond 0.00476 ( 12) SS BOND : angle 1.08839 ( 24) hydrogen bonds : bond 0.03070 ( 127) hydrogen bonds : angle 5.95645 ( 309) *********************** 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 162 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9445 (ptt90) cc_final: 0.9235 (ptm-80) REVERT: E 5 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9047 (tp-100) REVERT: E 6 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: E 87 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8539 (mttp) REVERT: A 359 ASP cc_start: 0.8795 (p0) cc_final: 0.8507 (p0) REVERT: A 366 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: A 401 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8560 (tt0) REVERT: A 485 PHE cc_start: 0.8485 (m-80) cc_final: 0.8218 (m-10) REVERT: D 77 ASN cc_start: 0.8992 (t0) cc_final: 0.8510 (t0) REVERT: D 80 TYR cc_start: 0.8268 (m-10) cc_final: 0.7975 (m-80) REVERT: D 103 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8363 (p) outliers start: 21 outliers final: 13 residues processed: 152 average time/residue: 0.0913 time to fit residues: 17.1683 Evaluate side-chains 148 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 425 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 375 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.4980 chunk 51 optimal weight: 0.0370 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN E 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079049 restraints weight = 13590.273| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 6.59 r_work: 0.2976 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5370 Z= 0.133 Angle : 0.681 8.493 7304 Z= 0.342 Chirality : 0.045 0.141 764 Planarity : 0.005 0.061 958 Dihedral : 4.925 22.300 746 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.21 % Favored : 91.34 % Rotamer: Outliers : 3.75 % Allowed : 20.54 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.31), residues: 658 helix: -4.11 (0.47), residues: 41 sheet: 0.54 (0.41), residues: 166 loop : -1.83 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 341 TYR 0.029 0.001 TYR E 111 PHE 0.018 0.001 PHE A 451 TRP 0.010 0.001 TRP B 431 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5358) covalent geometry : angle 0.67982 ( 7280) SS BOND : bond 0.00463 ( 12) SS BOND : angle 1.02749 ( 24) hydrogen bonds : bond 0.02920 ( 127) hydrogen bonds : angle 5.75753 ( 309) *********************** 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: 21 poor density : 136 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 ARG cc_start: 0.9432 (ptt90) cc_final: 0.9224 (ptm-80) REVERT: E 5 GLN cc_start: 0.9430 (tp-100) cc_final: 0.9047 (tp-100) REVERT: E 6 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: E 87 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8604 (mttp) REVERT: A 359 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8504 (p0) REVERT: A 366 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: A 401 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8551 (mt-10) REVERT: A 485 PHE cc_start: 0.8483 (m-80) cc_final: 0.8174 (m-10) REVERT: D 55 ASP cc_start: 0.9364 (m-30) cc_final: 0.9058 (p0) REVERT: D 77 ASN cc_start: 0.8914 (t0) cc_final: 0.8513 (t0) REVERT: D 80 TYR cc_start: 0.8316 (m-10) cc_final: 0.7952 (m-80) outliers start: 21 outliers final: 13 residues processed: 148 average time/residue: 0.1025 time to fit residues: 18.6255 Evaluate side-chains 145 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 425 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 359 ASP 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 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 32 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 5 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.099971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077009 restraints weight = 13732.244| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 6.06 r_work: 0.2917 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5370 Z= 0.246 Angle : 0.770 9.148 7304 Z= 0.392 Chirality : 0.048 0.157 764 Planarity : 0.005 0.061 958 Dihedral : 5.351 25.282 746 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.49 % Favored : 89.06 % Rotamer: Outliers : 3.75 % Allowed : 20.36 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.32), residues: 658 helix: -4.01 (0.54), residues: 35 sheet: 0.16 (0.40), residues: 178 loop : -1.74 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 119 TYR 0.031 0.002 TYR E 111 PHE 0.015 0.001 PHE A 451 TRP 0.011 0.002 TRP B 431 HIS 0.006 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 5358) covalent geometry : angle 0.76687 ( 7280) SS BOND : bond 0.00531 ( 12) SS BOND : angle 1.41338 ( 24) hydrogen bonds : bond 0.03412 ( 127) hydrogen bonds : angle 5.78958 ( 309) *********************** 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 154 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: B 401 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8737 (mt-10) REVERT: E 5 GLN cc_start: 0.9485 (tp-100) cc_final: 0.9111 (tp-100) REVERT: E 87 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8615 (mttp) REVERT: A 359 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8475 (p0) REVERT: A 366 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: A 381 LYS cc_start: 0.9598 (mmtm) cc_final: 0.8827 (tptp) REVERT: A 401 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8610 (mt-10) REVERT: A 427 CYS cc_start: 0.8585 (m) cc_final: 0.8303 (m) REVERT: D 77 ASN cc_start: 0.9061 (t0) cc_final: 0.8738 (t0) REVERT: D 80 TYR cc_start: 0.8502 (m-10) cc_final: 0.8084 (m-80) REVERT: D 117 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7432 (t80) outliers start: 21 outliers final: 13 residues processed: 147 average time/residue: 0.0969 time to fit residues: 17.5608 Evaluate side-chains 140 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 6 GLU 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 359 ASP Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 0.0060 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN ** D 5 GLN ** 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 = 0.3649 r_free = 0.3649 target = 0.101654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078774 restraints weight = 13502.192| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 6.13 r_work: 0.2956 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3811 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= 0.152 Angle : 0.752 9.197 7304 Z= 0.378 Chirality : 0.046 0.166 764 Planarity : 0.005 0.062 958 Dihedral : 5.018 23.199 746 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.21 % Favored : 91.34 % Rotamer: Outliers : 3.75 % Allowed : 22.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.32), residues: 658 helix: -4.01 (0.45), residues: 48 sheet: 0.05 (0.39), residues: 188 loop : -1.62 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 341 TYR 0.031 0.001 TYR E 111 PHE 0.014 0.001 PHE A 451 TRP 0.010 0.001 TRP B 431 HIS 0.005 0.002 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5358) covalent geometry : angle 0.74996 ( 7280) SS BOND : bond 0.00521 ( 12) SS BOND : angle 1.28987 ( 24) hydrogen bonds : bond 0.02940 ( 127) hydrogen bonds : angle 5.69857 ( 309) *********************** 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 158 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8658 (mt-10) REVERT: B 412 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8165 (t0) REVERT: E 5 GLN cc_start: 0.9485 (tp-100) cc_final: 0.9086 (tp-100) REVERT: E 6 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8802 (pt0) REVERT: E 87 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8537 (mttp) REVERT: A 341 ARG cc_start: 0.9269 (ttp80) cc_final: 0.8839 (ttp80) REVERT: A 359 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8461 (p0) REVERT: A 366 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: A 401 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8579 (tt0) REVERT: D 55 ASP cc_start: 0.9327 (m-30) cc_final: 0.9077 (p0) REVERT: D 77 ASN cc_start: 0.8957 (t0) cc_final: 0.8614 (t0) REVERT: D 80 TYR cc_start: 0.8491 (m-10) cc_final: 0.7958 (m-80) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.1032 time to fit residues: 18.8587 Evaluate side-chains 142 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 412 ASN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain E residue 6 GLU 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 374 CYS Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 510 PHE 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 40 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN ** D 5 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.077331 restraints weight = 13536.089| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 6.41 r_work: 0.2959 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3940 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= 0.160 Angle : 0.758 9.460 7304 Z= 0.381 Chirality : 0.046 0.151 764 Planarity : 0.005 0.063 958 Dihedral : 4.946 21.843 746 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % Rotamer: Outliers : 4.11 % Allowed : 22.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.32), residues: 658 helix: -3.95 (0.46), residues: 48 sheet: 0.22 (0.40), residues: 178 loop : -1.63 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 119 TYR 0.033 0.001 TYR E 111 PHE 0.013 0.001 PHE A 451 TRP 0.009 0.001 TRP B 431 HIS 0.005 0.002 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5358) covalent geometry : angle 0.75632 ( 7280) SS BOND : bond 0.00498 ( 12) SS BOND : angle 1.19947 ( 24) hydrogen bonds : bond 0.02936 ( 127) hydrogen bonds : angle 5.60968 ( 309) *********************** 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 154 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.9483 (tp-100) cc_final: 0.9075 (tp-100) REVERT: E 6 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8800 (pt0) REVERT: E 87 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8510 (mttp) REVERT: A 341 ARG cc_start: 0.9250 (ttp80) cc_final: 0.8829 (ttp80) REVERT: A 366 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: A 401 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: A 461 ARG cc_start: 0.9047 (ttm170) cc_final: 0.8674 (ttm110) REVERT: D 77 ASN cc_start: 0.8962 (t0) cc_final: 0.8655 (t0) REVERT: D 117 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7295 (t80) outliers start: 23 outliers final: 13 residues processed: 142 average time/residue: 0.0940 time to fit residues: 16.2542 Evaluate side-chains 141 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 6 GLU 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 E residue 121 GLN Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 HIS ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** 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 = 0.3618 r_free = 0.3618 target = 0.099614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077141 restraints weight = 13558.649| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 5.89 r_work: 0.2905 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 5370 Z= 0.251 Angle : 0.807 10.014 7304 Z= 0.411 Chirality : 0.048 0.168 764 Planarity : 0.005 0.061 958 Dihedral : 5.361 22.628 746 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.33 % Favored : 89.21 % Rotamer: Outliers : 4.29 % Allowed : 23.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.32), residues: 658 helix: -3.99 (0.44), residues: 48 sheet: 0.21 (0.40), residues: 178 loop : -1.64 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 119 TYR 0.035 0.001 TYR E 111 PHE 0.014 0.001 PHE A 324 TRP 0.009 0.001 TRP B 431 HIS 0.008 0.002 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 5358) covalent geometry : angle 0.80528 ( 7280) SS BOND : bond 0.00533 ( 12) SS BOND : angle 1.24685 ( 24) hydrogen bonds : bond 0.03569 ( 127) hydrogen bonds : angle 5.67407 ( 309) *********************** 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 150 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 LYS cc_start: 0.9013 (mtmm) cc_final: 0.8585 (mttp) REVERT: A 341 ARG cc_start: 0.9211 (ttp80) cc_final: 0.8767 (ttp80) REVERT: A 366 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: A 401 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: A 427 CYS cc_start: 0.8615 (m) cc_final: 0.8351 (m) REVERT: A 461 ARG cc_start: 0.8925 (ttm170) cc_final: 0.8563 (ttm110) REVERT: D 117 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7491 (t80) outliers start: 24 outliers final: 18 residues processed: 141 average time/residue: 0.1115 time to fit residues: 19.1064 Evaluate side-chains 143 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 PHE 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 6 GLU 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 E residue 121 GLN Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 HIS A 326 ASN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 82 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 = 0.3662 r_free = 0.3662 target = 0.102209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080034 restraints weight = 13501.708| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 6.11 r_work: 0.2957 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4194 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= 0.149 Angle : 0.802 10.574 7304 Z= 0.402 Chirality : 0.047 0.149 764 Planarity : 0.005 0.062 958 Dihedral : 5.089 20.740 746 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.51 % Favored : 91.03 % Rotamer: Outliers : 2.50 % Allowed : 25.89 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.32), residues: 658 helix: -3.75 (0.49), residues: 48 sheet: 0.62 (0.41), residues: 164 loop : -1.64 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 119 TYR 0.032 0.001 TYR E 111 PHE 0.013 0.001 PHE A 451 TRP 0.010 0.001 TRP B 431 HIS 0.005 0.002 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5358) covalent geometry : angle 0.80110 ( 7280) SS BOND : bond 0.00506 ( 12) SS BOND : angle 1.11504 ( 24) hydrogen bonds : bond 0.03153 ( 127) hydrogen bonds : angle 5.68424 ( 309) ********************** 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 : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 401 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8502 (pt0) REVERT: E 5 GLN cc_start: 0.9472 (tp-100) cc_final: 0.9078 (tp-100) REVERT: E 82 GLN cc_start: 0.9036 (tp40) cc_final: 0.8828 (tp40) REVERT: E 87 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8534 (mttp) REVERT: A 366 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: A 401 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: A 461 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8557 (ttm110) REVERT: A 495 THR cc_start: 0.9527 (p) cc_final: 0.9327 (p) REVERT: D 55 ASP cc_start: 0.9303 (m-30) cc_final: 0.9051 (p0) REVERT: D 90 ASP cc_start: 0.9036 (m-30) cc_final: 0.8694 (m-30) REVERT: D 117 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7330 (t80) outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 0.1044 time to fit residues: 18.1087 Evaluate side-chains 143 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 34 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain D residue 117 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 82 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 = 0.3658 r_free = 0.3658 target = 0.101902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079644 restraints weight = 13520.177| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 6.08 r_work: 0.2953 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4307 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= 0.162 Angle : 0.799 10.937 7304 Z= 0.401 Chirality : 0.047 0.148 764 Planarity : 0.005 0.062 958 Dihedral : 5.112 24.073 746 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.51 % Favored : 91.19 % Rotamer: Outliers : 3.57 % Allowed : 25.18 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.32), residues: 658 helix: -3.78 (0.48), residues: 48 sheet: 0.19 (0.40), residues: 178 loop : -1.53 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.032 0.001 TYR E 111 PHE 0.013 0.001 PHE A 451 TRP 0.009 0.001 TRP B 431 HIS 0.007 0.002 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5358) covalent geometry : angle 0.79728 ( 7280) SS BOND : bond 0.00501 ( 12) SS BOND : angle 1.10714 ( 24) hydrogen bonds : bond 0.03191 ( 127) hydrogen bonds : angle 5.59545 ( 309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2006.48 seconds wall clock time: 35 minutes 0.19 seconds (2100.19 seconds total)