Starting phenix.real_space_refine on Wed Sep 17 08:26:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blt_44676/09_2025/9blt_44676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blt_44676/09_2025/9blt_44676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blt_44676/09_2025/9blt_44676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blt_44676/09_2025/9blt_44676.map" model { file = "/net/cci-nas-00/data/ceres_data/9blt_44676/09_2025/9blt_44676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blt_44676/09_2025/9blt_44676.cif" } resolution = 3.38 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= 0.008 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 27 5.16 5 C 4459 2.51 5 N 1229 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7098 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4516 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 21, 'TRANS': 572} Chain: "B" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1270 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1259 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 1.56, per 1000 atoms: 0.22 Number of scatterers: 7098 At special positions: 0 Unit cell: (74.97, 122.745, 120.54, 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 27 16.00 O 1383 8.00 N 1229 7.00 C 4459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.57 Conformation dependent library (CDL) restraints added in 389.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 45.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 111 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 130 through 140 removed outlier: 4.318A pdb=" N LYS A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.609A pdb=" N GLY A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 274 through 294 removed outlier: 4.001A pdb=" N PHE A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 4.257A pdb=" N ARG A 391 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.712A pdb=" N ILE A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 556 through 568 removed outlier: 4.098A pdb=" N VAL A 562 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 597 Processing helix chain 'A' and resid 609 through 619 removed outlier: 4.104A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 102 removed outlier: 3.622A pdb=" N GLU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 125 removed outlier: 4.960A pdb=" N GLU B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 removed outlier: 3.834A pdb=" N HIS B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 124 removed outlier: 3.764A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.912A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.912A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL A 55 " --> pdb=" O MET A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 193 Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 268 removed outlier: 5.600A pdb=" N VAL A 264 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU A 256 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 382 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 333 removed outlier: 4.122A pdb=" N TYR A 331 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 340 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 458 removed outlier: 5.774A pdb=" N LYS A 456 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE A 447 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 458 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS A 485 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 468 through 472 Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.556A pdb=" N TYR B 199 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 191 through 196 removed outlier: 6.735A pdb=" N GLY B 212 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL B 194 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 210 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 160 through 163 removed outlier: 6.656A pdb=" N TYR C 199 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 180 removed outlier: 7.464A pdb=" N VAL C 213 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS C 180 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 210 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C 193 " --> pdb=" O GLY C 212 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1086 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: 1.10 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2400 1.34 - 1.46: 693 1.46 - 1.57: 4053 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 7191 Sorted by residual: bond pdb=" N THR A 474 " pdb=" CA THR A 474 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.34e-02 5.57e+03 6.82e+00 bond pdb=" N SER A 473 " pdb=" CA SER A 473 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.36e-02 5.41e+03 5.86e+00 bond pdb=" N ALA A 475 " pdb=" CA ALA A 475 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.18e-02 7.18e+03 3.37e+00 bond pdb=" N ARG B 207 " pdb=" CA ARG B 207 " ideal model delta sigma weight residual 1.457 1.435 0.022 1.41e-02 5.03e+03 2.41e+00 bond pdb=" CA SER A 473 " pdb=" CB SER A 473 " ideal model delta sigma weight residual 1.530 1.507 0.023 1.52e-02 4.33e+03 2.33e+00 ... (remaining 7186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 9491 1.42 - 2.83: 157 2.83 - 4.25: 39 4.25 - 5.66: 11 5.66 - 7.08: 2 Bond angle restraints: 9700 Sorted by residual: angle pdb=" CA THR A 474 " pdb=" C THR A 474 " pdb=" O THR A 474 " ideal model delta sigma weight residual 121.87 118.35 3.52 1.16e+00 7.43e-01 9.20e+00 angle pdb=" CA ALA A 475 " pdb=" C ALA A 475 " pdb=" O ALA A 475 " ideal model delta sigma weight residual 120.90 117.88 3.02 1.03e+00 9.43e-01 8.61e+00 angle pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " pdb=" CD GLU B 97 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.70e+00 3.46e-01 7.65e+00 angle pdb=" CA VAL A 546 " pdb=" CB VAL A 546 " pdb=" CG1 VAL A 546 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.45e+00 angle pdb=" N ILE B 130 " pdb=" CA ILE B 130 " pdb=" C ILE B 130 " ideal model delta sigma weight residual 106.21 109.02 -2.81 1.07e+00 8.73e-01 6.88e+00 ... (remaining 9695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3728 17.89 - 35.77: 521 35.77 - 53.66: 168 53.66 - 71.54: 34 71.54 - 89.42: 10 Dihedral angle restraints: 4461 sinusoidal: 1819 harmonic: 2642 Sorted by residual: dihedral pdb=" CB GLU B 113 " pdb=" CG GLU B 113 " pdb=" CD GLU B 113 " pdb=" OE1 GLU B 113 " ideal model delta sinusoidal sigma weight residual 0.00 89.42 -89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 309 " pdb=" CD ARG A 309 " pdb=" NE ARG A 309 " pdb=" CZ ARG A 309 " ideal model delta sinusoidal sigma weight residual -180.00 -136.02 -43.98 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB GLU A 382 " pdb=" CG GLU A 382 " pdb=" CD GLU A 382 " pdb=" OE1 GLU A 382 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 4458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 669 0.028 - 0.055: 290 0.055 - 0.083: 90 0.083 - 0.111: 67 0.111 - 0.138: 16 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CA ASN A 560 " pdb=" N ASN A 560 " pdb=" C ASN A 560 " pdb=" CB ASN A 560 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CB ILE A 633 " pdb=" CA ILE A 633 " pdb=" CG1 ILE A 633 " pdb=" CG2 ILE A 633 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 252 " pdb=" N ILE A 252 " pdb=" C ILE A 252 " pdb=" CB ILE A 252 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 1129 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 103 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 104 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 108 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C GLN A 108 " 0.020 2.00e-02 2.50e+03 pdb=" O GLN A 108 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA A 109 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 130 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 131 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.015 5.00e-02 4.00e+02 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 962 2.75 - 3.29: 6776 3.29 - 3.83: 11519 3.83 - 4.36: 12565 4.36 - 4.90: 23058 Nonbonded interactions: 54880 Sorted by model distance: nonbonded pdb=" OG SER A 444 " pdb=" O GLY A 489 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG A 391 " pdb=" OD2 ASP A 414 " model vdw 2.230 3.120 nonbonded pdb=" OD2 ASP A 536 " pdb=" OG1 THR A 539 " model vdw 2.237 3.040 nonbonded pdb=" O GLY A 528 " pdb=" OG SER A 550 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP A 556 " pdb=" ND2 ASN A 560 " model vdw 2.267 3.120 ... (remaining 54875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 59 through 217) selection = chain 'C' } 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: 3.840 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.003 0.036 7191 Z= 0.141 Angle : 0.513 7.078 9700 Z= 0.277 Chirality : 0.040 0.138 1132 Planarity : 0.003 0.041 1263 Dihedral : 18.586 89.425 2753 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.72 % Allowed : 32.77 % Favored : 64.51 % 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: 0.49 (0.29), residues: 913 helix: 1.83 (0.27), residues: 382 sheet: -0.39 (0.53), residues: 111 loop : -0.90 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.016 0.001 TYR B 78 PHE 0.009 0.001 PHE A 197 TRP 0.006 0.001 TRP A 126 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7191) covalent geometry : angle 0.51312 ( 9700) hydrogen bonds : bond 0.16285 ( 376) hydrogen bonds : angle 6.97317 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.252 Fit side-chains REVERT: A 108 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: A 252 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 348 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6066 (ttm-80) REVERT: B 127 LYS cc_start: 0.7619 (tttt) cc_final: 0.7055 (mptt) outliers start: 21 outliers final: 17 residues processed: 74 average time/residue: 0.0719 time to fit residues: 7.6408 Evaluate side-chains 74 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.200054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146820 restraints weight = 8818.130| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.41 r_work: 0.3598 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7191 Z= 0.232 Angle : 0.604 9.627 9700 Z= 0.317 Chirality : 0.045 0.167 1132 Planarity : 0.004 0.044 1263 Dihedral : 6.065 47.416 1001 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.35 % Allowed : 29.53 % Favored : 64.12 % 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: 0.19 (0.28), residues: 913 helix: 1.47 (0.25), residues: 386 sheet: -0.47 (0.51), residues: 120 loop : -1.00 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.013 0.002 TYR B 102 PHE 0.014 0.002 PHE B 179 TRP 0.005 0.002 TRP A 126 HIS 0.006 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 7191) covalent geometry : angle 0.60406 ( 9700) hydrogen bonds : bond 0.05391 ( 376) hydrogen bonds : angle 5.22470 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 59 time to evaluate : 0.334 Fit side-chains REVERT: A 108 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.6687 (pt0) REVERT: A 252 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8326 (tp) REVERT: B 78 TYR cc_start: 0.7209 (t80) cc_final: 0.6852 (t80) REVERT: B 90 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: B 127 LYS cc_start: 0.7644 (tttt) cc_final: 0.6952 (mptt) REVERT: B 128 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: B 129 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7937 (mp0) outliers start: 49 outliers final: 22 residues processed: 102 average time/residue: 0.0829 time to fit residues: 11.6373 Evaluate side-chains 81 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 136 HIS C 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.210946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.160377 restraints weight = 8898.052| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.20 r_work: 0.3756 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7191 Z= 0.166 Angle : 0.527 8.541 9700 Z= 0.276 Chirality : 0.043 0.157 1132 Planarity : 0.004 0.044 1263 Dihedral : 4.972 43.341 986 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.79 % Allowed : 30.44 % Favored : 64.77 % 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: 0.32 (0.28), residues: 913 helix: 1.65 (0.25), residues: 385 sheet: -0.53 (0.50), residues: 120 loop : -0.95 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 573 TYR 0.009 0.001 TYR A 243 PHE 0.025 0.002 PHE A 197 TRP 0.003 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7191) covalent geometry : angle 0.52653 ( 9700) hydrogen bonds : bond 0.04699 ( 376) hydrogen bonds : angle 4.91764 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 56 time to evaluate : 0.416 Fit side-chains REVERT: A 108 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.6584 (pt0) REVERT: A 252 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8265 (tp) REVERT: A 334 MET cc_start: 0.8065 (mmt) cc_final: 0.7808 (mmt) REVERT: A 348 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6233 (ttm-80) REVERT: A 556 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6774 (t0) REVERT: B 78 TYR cc_start: 0.7185 (t80) cc_final: 0.6827 (t80) REVERT: B 90 GLN cc_start: 0.7776 (mt0) cc_final: 0.7314 (mt0) REVERT: B 127 LYS cc_start: 0.7707 (tttt) cc_final: 0.7025 (mptt) REVERT: B 128 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: B 129 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7976 (mp0) outliers start: 37 outliers final: 26 residues processed: 85 average time/residue: 0.0702 time to fit residues: 8.7060 Evaluate side-chains 86 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.213022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162910 restraints weight = 8908.422| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.31 r_work: 0.3764 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7191 Z= 0.122 Angle : 0.479 7.924 9700 Z= 0.250 Chirality : 0.041 0.146 1132 Planarity : 0.003 0.041 1263 Dihedral : 4.688 41.940 986 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.05 % Allowed : 30.05 % Favored : 64.90 % 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: 0.55 (0.28), residues: 913 helix: 1.94 (0.25), residues: 386 sheet: -0.55 (0.50), residues: 120 loop : -0.89 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 405 TYR 0.009 0.001 TYR A 243 PHE 0.016 0.001 PHE A 197 TRP 0.002 0.001 TRP A 126 HIS 0.002 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7191) covalent geometry : angle 0.47941 ( 9700) hydrogen bonds : bond 0.04138 ( 376) hydrogen bonds : angle 4.66211 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 52 time to evaluate : 0.289 Fit side-chains REVERT: A 108 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.6525 (pt0) REVERT: A 252 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 348 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6171 (ttm-80) REVERT: A 556 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6764 (t0) REVERT: B 78 TYR cc_start: 0.7157 (t80) cc_final: 0.6770 (t80) REVERT: B 90 GLN cc_start: 0.7756 (mt0) cc_final: 0.7295 (mt0) REVERT: B 127 LYS cc_start: 0.7683 (tttt) cc_final: 0.7064 (mptt) REVERT: B 129 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7976 (mp0) REVERT: B 201 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7484 (pp) outliers start: 39 outliers final: 21 residues processed: 82 average time/residue: 0.0704 time to fit residues: 8.5642 Evaluate side-chains 76 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.0570 chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.0338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.199548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145294 restraints weight = 8896.631| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.46 r_work: 0.3593 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7191 Z= 0.152 Angle : 0.506 8.261 9700 Z= 0.262 Chirality : 0.042 0.151 1132 Planarity : 0.003 0.040 1263 Dihedral : 4.730 42.100 985 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.66 % Allowed : 29.92 % Favored : 65.41 % 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: 0.50 (0.28), residues: 913 helix: 1.89 (0.25), residues: 386 sheet: -0.65 (0.49), residues: 119 loop : -0.90 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.013 0.001 TYR A 243 PHE 0.031 0.001 PHE A 197 TRP 0.003 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7191) covalent geometry : angle 0.50559 ( 9700) hydrogen bonds : bond 0.04274 ( 376) hydrogen bonds : angle 4.63382 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 0.280 Fit side-chains REVERT: A 108 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.6498 (pt0) REVERT: A 252 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8230 (tp) REVERT: A 348 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6428 (ttp-170) REVERT: A 556 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6833 (t0) REVERT: B 78 TYR cc_start: 0.7106 (t80) cc_final: 0.6748 (t80) REVERT: B 90 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7318 (mt0) REVERT: B 127 LYS cc_start: 0.7650 (tttt) cc_final: 0.6961 (mptt) REVERT: B 128 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: B 129 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7987 (mp0) REVERT: B 201 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7379 (pp) outliers start: 36 outliers final: 24 residues processed: 82 average time/residue: 0.0719 time to fit residues: 8.6098 Evaluate side-chains 83 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.200583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.146987 restraints weight = 8852.162| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.05 r_work: 0.3570 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7191 Z= 0.120 Angle : 0.487 7.792 9700 Z= 0.250 Chirality : 0.041 0.145 1132 Planarity : 0.003 0.039 1263 Dihedral : 4.579 41.156 985 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.79 % Allowed : 30.18 % Favored : 65.03 % 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: 0.65 (0.28), residues: 913 helix: 2.07 (0.25), residues: 386 sheet: -0.62 (0.50), residues: 119 loop : -0.85 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.010 0.001 TYR A 243 PHE 0.022 0.001 PHE A 197 TRP 0.002 0.001 TRP A 126 HIS 0.002 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7191) covalent geometry : angle 0.48717 ( 9700) hydrogen bonds : bond 0.03939 ( 376) hydrogen bonds : angle 4.48899 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 56 time to evaluate : 0.293 Fit side-chains REVERT: A 108 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: A 252 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 348 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6341 (ttp-170) REVERT: A 556 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6877 (t0) REVERT: B 78 TYR cc_start: 0.6885 (t80) cc_final: 0.6518 (t80) REVERT: B 90 GLN cc_start: 0.7619 (mt0) cc_final: 0.7174 (mt0) REVERT: B 91 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7301 (ttm170) REVERT: B 127 LYS cc_start: 0.7581 (tttt) cc_final: 0.6923 (mptt) REVERT: B 128 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: B 129 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7928 (mp0) REVERT: B 201 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7224 (pp) outliers start: 37 outliers final: 23 residues processed: 86 average time/residue: 0.0882 time to fit residues: 10.3900 Evaluate side-chains 81 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.199954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145523 restraints weight = 8841.453| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.72 r_work: 0.3576 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7191 Z= 0.136 Angle : 0.517 9.783 9700 Z= 0.264 Chirality : 0.041 0.148 1132 Planarity : 0.004 0.041 1263 Dihedral : 4.611 41.125 985 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.27 % Allowed : 30.18 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.28), residues: 913 helix: 2.01 (0.25), residues: 390 sheet: -0.66 (0.50), residues: 119 loop : -0.87 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.013 0.001 TYR A 243 PHE 0.021 0.001 PHE A 197 TRP 0.005 0.001 TRP A 126 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7191) covalent geometry : angle 0.51672 ( 9700) hydrogen bonds : bond 0.04026 ( 376) hydrogen bonds : angle 4.47494 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 0.285 Fit side-chains REVERT: A 108 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.6498 (tt0) REVERT: A 252 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8225 (tp) REVERT: A 348 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6405 (ttp-170) REVERT: A 556 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6806 (t0) REVERT: B 78 TYR cc_start: 0.7116 (t80) cc_final: 0.6757 (t80) REVERT: B 90 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: B 91 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7435 (ttm170) REVERT: B 127 LYS cc_start: 0.7606 (tttt) cc_final: 0.6958 (mptt) REVERT: B 128 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: B 129 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7997 (mp0) REVERT: B 201 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7373 (pp) outliers start: 33 outliers final: 24 residues processed: 78 average time/residue: 0.0916 time to fit residues: 9.9859 Evaluate side-chains 84 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 72 optimal weight: 0.0470 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.199467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.146142 restraints weight = 8847.332| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.60 r_work: 0.3575 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7191 Z= 0.145 Angle : 0.517 8.122 9700 Z= 0.265 Chirality : 0.042 0.150 1132 Planarity : 0.003 0.038 1263 Dihedral : 4.658 41.346 985 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.53 % Allowed : 29.66 % Favored : 65.80 % 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: 0.58 (0.28), residues: 913 helix: 1.97 (0.25), residues: 390 sheet: -0.63 (0.49), residues: 121 loop : -0.87 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.013 0.001 TYR A 243 PHE 0.021 0.001 PHE A 197 TRP 0.005 0.001 TRP A 126 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7191) covalent geometry : angle 0.51663 ( 9700) hydrogen bonds : bond 0.04118 ( 376) hydrogen bonds : angle 4.47720 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.285 Fit side-chains REVERT: A 108 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.6496 (pt0) REVERT: A 252 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8196 (tp) REVERT: A 348 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6424 (ttp-170) REVERT: B 90 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7331 (mt0) REVERT: B 91 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7505 (ttm170) REVERT: B 127 LYS cc_start: 0.7610 (tttt) cc_final: 0.6973 (mptt) REVERT: B 128 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: B 129 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7990 (mp0) REVERT: B 201 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7381 (pp) outliers start: 35 outliers final: 25 residues processed: 82 average time/residue: 0.0779 time to fit residues: 8.9644 Evaluate side-chains 85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.200151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145838 restraints weight = 8840.766| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.71 r_work: 0.3602 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7191 Z= 0.129 Angle : 0.510 7.883 9700 Z= 0.262 Chirality : 0.041 0.148 1132 Planarity : 0.003 0.038 1263 Dihedral : 4.580 40.955 985 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.40 % Allowed : 29.79 % Favored : 65.80 % 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: 0.65 (0.28), residues: 913 helix: 2.06 (0.25), residues: 390 sheet: -0.68 (0.49), residues: 118 loop : -0.86 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.016 0.001 TYR B 78 PHE 0.020 0.001 PHE A 197 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7191) covalent geometry : angle 0.51015 ( 9700) hydrogen bonds : bond 0.03953 ( 376) hydrogen bonds : angle 4.41984 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.287 Fit side-chains REVERT: A 108 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.6552 (tt0) REVERT: A 252 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8182 (tp) REVERT: A 348 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6403 (ttp-170) REVERT: B 90 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: B 91 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7422 (ttm170) REVERT: B 127 LYS cc_start: 0.7589 (tttt) cc_final: 0.6980 (mptt) REVERT: B 128 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: B 129 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8003 (mp0) REVERT: B 201 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7338 (pp) outliers start: 34 outliers final: 26 residues processed: 80 average time/residue: 0.0855 time to fit residues: 9.4718 Evaluate side-chains 86 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 0.2980 chunk 30 optimal weight: 0.0070 chunk 45 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.202119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.146524 restraints weight = 8833.714| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.96 r_work: 0.3578 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7191 Z= 0.106 Angle : 0.489 7.349 9700 Z= 0.252 Chirality : 0.040 0.140 1132 Planarity : 0.003 0.039 1263 Dihedral : 4.382 39.442 985 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.85 % Allowed : 31.35 % Favored : 65.80 % 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: 0.81 (0.28), residues: 913 helix: 2.25 (0.26), residues: 390 sheet: -0.59 (0.49), residues: 119 loop : -0.83 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.013 0.001 TYR B 78 PHE 0.018 0.001 PHE A 197 TRP 0.004 0.001 TRP A 126 HIS 0.002 0.000 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7191) covalent geometry : angle 0.48923 ( 9700) hydrogen bonds : bond 0.03587 ( 376) hydrogen bonds : angle 4.28342 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.316 Fit side-chains REVERT: A 108 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: A 348 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6325 (ttp-170) REVERT: B 127 LYS cc_start: 0.7592 (tttt) cc_final: 0.7007 (mptt) REVERT: B 129 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8018 (mp0) REVERT: B 201 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7206 (pp) outliers start: 22 outliers final: 17 residues processed: 73 average time/residue: 0.0770 time to fit residues: 7.9860 Evaluate side-chains 73 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 49 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.201911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147638 restraints weight = 8912.139| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.47 r_work: 0.3647 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7191 Z= 0.112 Angle : 0.492 7.485 9700 Z= 0.253 Chirality : 0.040 0.140 1132 Planarity : 0.003 0.035 1263 Dihedral : 4.271 39.268 982 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.98 % Allowed : 31.22 % Favored : 65.80 % 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: 0.88 (0.29), residues: 913 helix: 2.35 (0.26), residues: 390 sheet: -0.57 (0.49), residues: 119 loop : -0.84 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.013 0.001 TYR B 78 PHE 0.018 0.001 PHE A 197 TRP 0.005 0.001 TRP A 126 HIS 0.002 0.000 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7191) covalent geometry : angle 0.49201 ( 9700) hydrogen bonds : bond 0.03576 ( 376) hydrogen bonds : angle 4.24872 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.74 seconds wall clock time: 40 minutes 47.41 seconds (2447.41 seconds total)