Starting phenix.real_space_refine on Wed Aug 5 14:13:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcc_64952/08_2026/9vcc_64952.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcc_64952/08_2026/9vcc_64952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vcc_64952/08_2026/9vcc_64952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcc_64952/08_2026/9vcc_64952.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vcc_64952/08_2026/9vcc_64952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcc_64952/08_2026/9vcc_64952.map" } resolution = 3.92 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= 0.002 sd= 0.030 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 56 5.16 5 C 6345 2.51 5 N 1697 2.21 5 O 1813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9911 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5074 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 37, 'TRANS': 601} Chain: "A" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4837 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 33, 'TRANS': 570} Time building chain proxies: 2.18, per 1000 atoms: 0.22 Number of scatterers: 9911 At special positions: 0 Unit cell: (98.77, 100.43, 130.31, 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 56 16.00 O 1813 8.00 N 1697 7.00 C 6345 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: 1.25 Conformation dependent library (CDL) restraints added in 508.0 milliseconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 56.2% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 89 through 103 removed outlier: 3.568A pdb=" N ARG B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.664A pdb=" N TYR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 134 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 154 through 170 Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 171 through 183 removed outlier: 5.317A pdb=" N ASP B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.829A pdb=" N ARG B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.628A pdb=" N HIS B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 292 through 298 removed outlier: 4.292A pdb=" N MET B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 296 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 297 " --> pdb=" O GLN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.731A pdb=" N TRP B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 400 through 413 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.774A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 513 through 524 removed outlier: 3.580A pdb=" N ILE B 517 " --> pdb=" O THR B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 539 Processing helix chain 'B' and resid 553 through 562 Processing helix chain 'B' and resid 567 through 577 Processing helix chain 'B' and resid 583 through 600 removed outlier: 3.842A pdb=" N CYS B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 621 through 643 Processing helix chain 'B' and resid 651 through 672 removed outlier: 3.661A pdb=" N ASN B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'A' and resid 89 through 103 removed outlier: 3.854A pdb=" N ARG A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.517A pdb=" N GLN A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 170 through 182 removed outlier: 4.376A pdb=" N ASP A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 233 through 247 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.724A pdb=" N CYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 Processing helix chain 'A' and resid 621 through 646 Processing helix chain 'A' and resid 651 through 671 Processing helix chain 'A' and resid 672 through 684 Processing sheet with id=AA1, first strand: chain 'B' and resid 271 through 275 removed outlier: 3.669A pdb=" N GLY B 231 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N GLU B 316 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU B 286 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS B 318 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA B 288 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS B 320 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 290 " --> pdb=" O CYS B 320 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 201 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 319 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE B 203 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 351 through 353 Processing sheet with id=AA3, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 254 removed outlier: 3.637A pdb=" N ASP A 291 " --> pdb=" O CYS A 230 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 202 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG A 343 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE A 204 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 353 removed outlier: 3.785A pdb=" N THR A 484 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 439 " --> pdb=" O CYS A 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448 508 hydrogen bonds defined for protein. 1485 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: 1.95 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3243 1.34 - 1.46: 2209 1.46 - 1.58: 4599 1.58 - 1.70: 3 1.70 - 1.82: 84 Bond restraints: 10138 Sorted by residual: bond pdb=" CG PRO A 193 " pdb=" CD PRO A 193 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.19e+01 bond pdb=" CB PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 1.492 1.687 -0.195 5.00e-02 4.00e+02 1.51e+01 bond pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.58e+00 bond pdb=" CG PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 1.503 1.424 0.079 3.40e-02 8.65e+02 5.41e+00 bond pdb=" CB PRO A 193 " pdb=" CG PRO A 193 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.00e+00 ... (remaining 10133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 13609 3.05 - 6.10: 93 6.10 - 9.15: 25 9.15 - 12.20: 6 12.20 - 15.25: 2 Bond angle restraints: 13735 Sorted by residual: angle pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" CD PRO A 565 " ideal model delta sigma weight residual 112.00 96.75 15.25 1.40e+00 5.10e-01 1.19e+02 angle pdb=" CA PRO A 193 " pdb=" N PRO A 193 " pdb=" CD PRO A 193 " ideal model delta sigma weight residual 112.00 99.64 12.36 1.40e+00 5.10e-01 7.79e+01 angle pdb=" N PRO A 193 " pdb=" CD PRO A 193 " pdb=" CG PRO A 193 " ideal model delta sigma weight residual 103.20 91.12 12.08 1.50e+00 4.44e-01 6.49e+01 angle pdb=" N PRO A 565 " pdb=" CD PRO A 565 " pdb=" CG PRO A 565 " ideal model delta sigma weight residual 103.20 93.74 9.46 1.50e+00 4.44e-01 3.98e+01 angle pdb=" CA PRO B 59 " pdb=" N PRO B 59 " pdb=" CD PRO B 59 " ideal model delta sigma weight residual 112.00 103.52 8.48 1.40e+00 5.10e-01 3.67e+01 ... (remaining 13730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 5341 17.04 - 34.08: 615 34.08 - 51.12: 153 51.12 - 68.16: 60 68.16 - 85.20: 9 Dihedral angle restraints: 6178 sinusoidal: 2533 harmonic: 3645 Sorted by residual: dihedral pdb=" CA LYS B 104 " pdb=" C LYS B 104 " pdb=" N GLU B 105 " pdb=" CA GLU B 105 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA VAL A 670 " pdb=" C VAL A 670 " pdb=" N HIS A 671 " pdb=" CA HIS A 671 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ILE B 561 " pdb=" C ILE B 561 " pdb=" N GLN B 562 " pdb=" CA GLN B 562 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 6175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1266 0.053 - 0.105: 227 0.105 - 0.158: 36 0.158 - 0.210: 5 0.210 - 0.263: 1 Chirality restraints: 1535 Sorted by residual: chirality pdb=" CB ILE A 673 " pdb=" CA ILE A 673 " pdb=" CG1 ILE A 673 " pdb=" CG2 ILE A 673 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO A 565 " pdb=" N PRO A 565 " pdb=" C PRO A 565 " pdb=" CB PRO A 565 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA MET B 519 " pdb=" N MET B 519 " pdb=" C MET B 519 " pdb=" CB MET B 519 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 1532 not shown) Planarity restraints: 1771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 192 " -0.080 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A 193 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 564 " -0.080 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO A 565 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 58 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO B 59 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.058 5.00e-02 4.00e+02 ... (remaining 1768 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 249 2.66 - 3.22: 10353 3.22 - 3.78: 17820 3.78 - 4.34: 23483 4.34 - 4.90: 34873 Nonbonded interactions: 86778 Sorted by model distance: nonbonded pdb=" O SER A 588 " pdb=" NE2 GLN A 592 " model vdw 2.097 3.120 nonbonded pdb=" OG SER A 360 " pdb=" OD1 ASP A 362 " model vdw 2.151 3.040 nonbonded pdb=" OG SER A 374 " pdb=" OD1 ASN A 376 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 226 " pdb=" OE1 GLU A 286 " model vdw 2.224 3.040 nonbonded pdb=" O PRO A 512 " pdb=" OH TYR A 572 " model vdw 2.224 3.040 ... (remaining 86773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 85 through 688) } 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 group one per residue 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: 1.760 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.040 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 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 : 0.004 0.195 10138 Z= 0.169 Angle : 0.771 15.253 13735 Z= 0.425 Chirality : 0.042 0.263 1535 Planarity : 0.006 0.112 1771 Dihedral : 16.328 85.200 3814 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.37 % Allowed : 24.93 % Favored : 74.70 % 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 are not related in a simple way. whole: -0.31 (0.24), residues: 1239 helix: 0.73 (0.20), residues: 650 sheet: -1.01 (0.57), residues: 93 loop : -1.26 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 571 TYR 0.016 0.001 TYR B 572 PHE 0.026 0.002 PHE A 539 TRP 0.026 0.002 TRP B 305 HIS 0.012 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.17 (10138) covalent geometry : angle 0.77090 / 0.42 (13735) hydrogen bonds : bond 0.15665 / 10.06 ( 508) hydrogen bonds : angle 6.20270 / 4.45 ( 1485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 667 GLN cc_start: 0.7488 (mt0) cc_final: 0.6759 (mp10) REVERT: A 626 MET cc_start: 0.8391 (mmp) cc_final: 0.8186 (mmm) outliers start: 4 outliers final: 2 residues processed: 103 average time/residue: 0.0938 time to fit residues: 13.5527 Evaluate side-chains 99 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 486 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS A 541 GLN ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 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 = 0.4587 r_free = 0.4587 target = 0.130432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.106744 restraints weight = 42363.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.108682 restraints weight = 33430.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.110149 restraints weight = 26836.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.111193 restraints weight = 22925.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.111600 restraints weight = 20332.323| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10138 Z= 0.177 Angle : 0.649 9.352 13735 Z= 0.336 Chirality : 0.043 0.192 1535 Planarity : 0.005 0.050 1771 Dihedral : 4.522 39.058 1353 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.38 % Allowed : 21.92 % Favored : 74.70 % 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 are not related in a simple way. whole: -0.43 (0.24), residues: 1239 helix: 0.71 (0.20), residues: 662 sheet: -1.22 (0.54), residues: 91 loop : -1.44 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.016 0.002 TYR A 396 PHE 0.042 0.002 PHE A 593 TRP 0.012 0.002 TRP B 640 HIS 0.009 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (10138) covalent geometry : angle 0.64856 / 0.34 (13735) hydrogen bonds : bond 0.04481 / 2.96 ( 508) hydrogen bonds : angle 5.34152 / 3.86 ( 1485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 470 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7426 (mmm-85) REVERT: B 480 GLU cc_start: 0.8814 (pm20) cc_final: 0.8382 (pm20) REVERT: A 592 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7512 (mm-40) outliers start: 37 outliers final: 19 residues processed: 130 average time/residue: 0.0858 time to fit residues: 16.1833 Evaluate side-chains 115 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 632 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 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 = 0.4586 r_free = 0.4586 target = 0.130951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.110923 restraints weight = 50456.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.113417 restraints weight = 35385.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.114973 restraints weight = 26715.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.116019 restraints weight = 21697.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.116479 restraints weight = 18838.725| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10138 Z= 0.187 Angle : 0.664 9.059 13735 Z= 0.341 Chirality : 0.043 0.174 1535 Planarity : 0.005 0.053 1771 Dihedral : 4.507 20.246 1349 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.84 % Allowed : 21.92 % Favored : 73.24 % 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 are not related in a simple way. whole: -0.59 (0.23), residues: 1239 helix: 0.60 (0.20), residues: 663 sheet: -1.59 (0.51), residues: 92 loop : -1.49 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 595 TYR 0.014 0.002 TYR B 572 PHE 0.025 0.002 PHE A 539 TRP 0.012 0.002 TRP B 640 HIS 0.009 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (10138) covalent geometry : angle 0.66398 / 0.34 (13735) hydrogen bonds : bond 0.04531 / 2.95 ( 508) hydrogen bonds : angle 5.27836 / 3.80 ( 1485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 100 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 480 GLU cc_start: 0.8763 (pm20) cc_final: 0.8367 (pm20) REVERT: B 644 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7933 (ptp90) REVERT: A 98 ASP cc_start: 0.8475 (m-30) cc_final: 0.8224 (p0) REVERT: A 626 MET cc_start: 0.7801 (mmm) cc_final: 0.7473 (mmp) outliers start: 53 outliers final: 37 residues processed: 145 average time/residue: 0.0880 time to fit residues: 18.1320 Evaluate side-chains 134 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 632 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.131301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.111043 restraints weight = 50496.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.113479 restraints weight = 34884.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.115008 restraints weight = 26349.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.116217 restraints weight = 21511.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.116848 restraints weight = 18472.400| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10138 Z= 0.165 Angle : 0.644 9.848 13735 Z= 0.328 Chirality : 0.042 0.166 1535 Planarity : 0.005 0.053 1771 Dihedral : 4.482 20.334 1349 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.66 % Allowed : 22.83 % Favored : 72.51 % 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 are not related in a simple way. whole: -0.59 (0.24), residues: 1239 helix: 0.65 (0.20), residues: 663 sheet: -1.71 (0.49), residues: 99 loop : -1.53 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 595 TYR 0.015 0.002 TYR A 572 PHE 0.028 0.002 PHE A 539 TRP 0.027 0.002 TRP B 305 HIS 0.008 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (10138) covalent geometry : angle 0.64427 / 0.33 (13735) hydrogen bonds : bond 0.04145 / 2.69 ( 508) hydrogen bonds : angle 5.18426 / 3.73 ( 1485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 98 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 470 ARG cc_start: 0.7977 (mmt180) cc_final: 0.7263 (mmm-85) REVERT: B 480 GLU cc_start: 0.8795 (pm20) cc_final: 0.8378 (pm20) REVERT: B 519 MET cc_start: 0.8447 (pmm) cc_final: 0.8089 (pmm) REVERT: B 546 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: B 644 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8036 (ptp90) REVERT: A 531 ASN cc_start: 0.7630 (t0) cc_final: 0.7212 (t0) REVERT: A 592 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7438 (mm110) REVERT: A 626 MET cc_start: 0.7917 (mmm) cc_final: 0.7564 (mmp) outliers start: 51 outliers final: 38 residues processed: 138 average time/residue: 0.0902 time to fit residues: 17.8802 Evaluate side-chains 133 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 672 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.130186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.109541 restraints weight = 50506.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.111840 restraints weight = 34693.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.113549 restraints weight = 26380.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.114733 restraints weight = 21534.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.115252 restraints weight = 18692.562| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10138 Z= 0.194 Angle : 0.671 10.352 13735 Z= 0.342 Chirality : 0.043 0.175 1535 Planarity : 0.005 0.057 1771 Dihedral : 4.522 20.993 1349 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.03 % Allowed : 22.28 % Favored : 71.69 % 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 are not related in a simple way. whole: -0.67 (0.23), residues: 1239 helix: 0.59 (0.19), residues: 664 sheet: -1.82 (0.49), residues: 100 loop : -1.57 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 595 TYR 0.015 0.002 TYR A 396 PHE 0.026 0.002 PHE A 539 TRP 0.025 0.002 TRP B 305 HIS 0.007 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (10138) covalent geometry : angle 0.67149 / 0.34 (13735) hydrogen bonds : bond 0.04288 / 2.78 ( 508) hydrogen bonds : angle 5.26391 / 3.79 ( 1485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 96 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 470 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7154 (mmm-85) REVERT: B 519 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8161 (pmm) REVERT: B 546 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: B 644 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7978 (ptp90) REVERT: A 429 MET cc_start: 0.2592 (mmm) cc_final: 0.2320 (mmm) REVERT: A 520 PHE cc_start: 0.5173 (OUTLIER) cc_final: 0.4754 (t80) REVERT: A 531 ASN cc_start: 0.7696 (t0) cc_final: 0.7347 (t0) REVERT: A 592 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7492 (mm110) REVERT: A 626 MET cc_start: 0.8062 (mmm) cc_final: 0.7699 (mmp) outliers start: 66 outliers final: 53 residues processed: 150 average time/residue: 0.0934 time to fit residues: 19.8615 Evaluate side-chains 152 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 GLN A 672 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.135584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.116399 restraints weight = 49925.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.118677 restraints weight = 34072.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.119904 restraints weight = 25819.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.121277 restraints weight = 20546.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.122151 restraints weight = 18050.381| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10138 Z= 0.124 Angle : 0.618 8.898 13735 Z= 0.309 Chirality : 0.042 0.167 1535 Planarity : 0.005 0.044 1771 Dihedral : 4.349 19.778 1349 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.11 % Allowed : 24.84 % Favored : 71.05 % 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 are not related in a simple way. whole: -0.32 (0.24), residues: 1239 helix: 0.87 (0.20), residues: 658 sheet: -1.86 (0.46), residues: 111 loop : -1.29 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.013 0.001 TYR A 396 PHE 0.031 0.002 PHE A 539 TRP 0.033 0.002 TRP B 305 HIS 0.008 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10138) covalent geometry : angle 0.61765 / 0.31 (13735) hydrogen bonds : bond 0.03750 / 2.43 ( 508) hydrogen bonds : angle 4.95594 / 3.56 ( 1485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 429 MET cc_start: 0.5645 (mmm) cc_final: 0.5192 (mmm) REVERT: B 470 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7203 (mmm-85) REVERT: B 480 GLU cc_start: 0.8701 (pm20) cc_final: 0.8275 (pm20) REVERT: B 519 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8045 (pmm) REVERT: B 546 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: B 644 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7803 (ptp90) REVERT: B 667 GLN cc_start: 0.7703 (mt0) cc_final: 0.7179 (mp10) REVERT: A 303 TRP cc_start: 0.7281 (p-90) cc_final: 0.6976 (p-90) REVERT: A 592 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7387 (mm110) REVERT: A 625 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7682 (pt) REVERT: A 626 MET cc_start: 0.8051 (mmm) cc_final: 0.7629 (mmp) outliers start: 45 outliers final: 30 residues processed: 141 average time/residue: 0.0967 time to fit residues: 19.1350 Evaluate side-chains 132 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 672 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 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 = 0.4605 r_free = 0.4605 target = 0.131315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.111361 restraints weight = 50828.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.113660 restraints weight = 34965.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.114921 restraints weight = 26617.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.116190 restraints weight = 22497.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.116708 restraints weight = 19438.519| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10138 Z= 0.187 Angle : 0.688 10.510 13735 Z= 0.347 Chirality : 0.043 0.201 1535 Planarity : 0.005 0.050 1771 Dihedral : 4.416 20.600 1349 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.11 % Allowed : 24.47 % Favored : 70.41 % 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 are not related in a simple way. whole: -0.47 (0.24), residues: 1239 helix: 0.73 (0.20), residues: 664 sheet: -1.81 (0.48), residues: 100 loop : -1.43 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 610 TYR 0.015 0.002 TYR A 396 PHE 0.024 0.002 PHE A 539 TRP 0.020 0.002 TRP B 305 HIS 0.009 0.001 HIS A 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (10138) covalent geometry : angle 0.68767 / 0.35 (13735) hydrogen bonds : bond 0.04070 / 2.61 ( 508) hydrogen bonds : angle 5.13028 / 3.68 ( 1485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8281 (p0) REVERT: B 429 MET cc_start: 0.5603 (mmm) cc_final: 0.5055 (mmm) REVERT: B 470 ARG cc_start: 0.7943 (mmt180) cc_final: 0.7137 (mmm-85) REVERT: B 519 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8090 (pmm) REVERT: B 533 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7774 (pt) REVERT: B 546 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6365 (m-80) REVERT: B 582 LYS cc_start: 0.8323 (tmtt) cc_final: 0.7924 (tmtm) REVERT: B 644 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7892 (ptp90) REVERT: B 667 GLN cc_start: 0.7814 (mt0) cc_final: 0.7127 (mp10) REVERT: A 429 MET cc_start: 0.2964 (mmm) cc_final: 0.2728 (mmm) REVERT: A 520 PHE cc_start: 0.5183 (OUTLIER) cc_final: 0.4805 (t80) REVERT: A 531 ASN cc_start: 0.7533 (t0) cc_final: 0.7149 (t0) REVERT: A 592 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7402 (mm110) REVERT: A 626 MET cc_start: 0.8228 (mmm) cc_final: 0.7801 (mmp) REVERT: A 644 ARG cc_start: 0.5558 (mmp-170) cc_final: 0.5256 (mmm160) outliers start: 56 outliers final: 46 residues processed: 145 average time/residue: 0.0892 time to fit residues: 18.4222 Evaluate side-chains 144 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 92 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.131584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.111765 restraints weight = 50609.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.114046 restraints weight = 34861.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.115409 restraints weight = 26681.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.116615 restraints weight = 22232.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.117066 restraints weight = 19184.959| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10138 Z= 0.169 Angle : 0.696 12.377 13735 Z= 0.347 Chirality : 0.043 0.165 1535 Planarity : 0.005 0.048 1771 Dihedral : 4.456 20.709 1349 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.12 % Allowed : 23.84 % Favored : 70.05 % 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 are not related in a simple way. whole: -0.61 (0.24), residues: 1239 helix: 0.63 (0.20), residues: 663 sheet: -1.95 (0.47), residues: 102 loop : -1.47 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 610 TYR 0.015 0.002 TYR A 396 PHE 0.028 0.002 PHE A 539 TRP 0.042 0.002 TRP B 305 HIS 0.007 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (10138) covalent geometry : angle 0.69577 / 0.35 (13735) hydrogen bonds : bond 0.04065 / 2.60 ( 508) hydrogen bonds : angle 5.15758 / 3.70 ( 1485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 95 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8339 (p0) REVERT: B 429 MET cc_start: 0.5746 (mmm) cc_final: 0.5060 (mmm) REVERT: B 470 ARG cc_start: 0.7971 (mmt180) cc_final: 0.7160 (mmm-85) REVERT: B 480 GLU cc_start: 0.8766 (pm20) cc_final: 0.8378 (pm20) REVERT: B 519 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8104 (pmm) REVERT: B 533 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7781 (pt) REVERT: B 546 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: B 644 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7889 (ptp90) REVERT: B 667 GLN cc_start: 0.7856 (mt0) cc_final: 0.7284 (mp10) REVERT: A 278 MET cc_start: 0.7879 (tmm) cc_final: 0.7586 (tmm) REVERT: A 520 PHE cc_start: 0.5125 (OUTLIER) cc_final: 0.4746 (t80) REVERT: A 531 ASN cc_start: 0.7547 (t0) cc_final: 0.7182 (t0) REVERT: A 592 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7412 (mm110) REVERT: A 626 MET cc_start: 0.8319 (mmm) cc_final: 0.7907 (mmp) REVERT: A 681 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7693 (tm-30) outliers start: 67 outliers final: 50 residues processed: 153 average time/residue: 0.0884 time to fit residues: 19.3473 Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 91 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 681 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.134634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.115059 restraints weight = 50580.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.117462 restraints weight = 34924.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.119036 restraints weight = 26451.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.119976 restraints weight = 21699.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.120398 restraints weight = 18955.326| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10138 Z= 0.130 Angle : 0.674 9.906 13735 Z= 0.333 Chirality : 0.042 0.165 1535 Planarity : 0.005 0.053 1771 Dihedral : 4.326 19.831 1349 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.38 % Allowed : 25.94 % Favored : 69.68 % 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 are not related in a simple way. whole: -0.40 (0.24), residues: 1239 helix: 0.81 (0.20), residues: 657 sheet: -1.98 (0.45), residues: 111 loop : -1.31 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.021 0.001 TYR A 638 PHE 0.029 0.002 PHE A 539 TRP 0.030 0.002 TRP B 305 HIS 0.011 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10138) covalent geometry : angle 0.67444 / 0.33 (13735) hydrogen bonds : bond 0.03757 / 2.40 ( 508) hydrogen bonds : angle 4.99593 / 3.60 ( 1485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 429 MET cc_start: 0.5691 (mmm) cc_final: 0.5074 (mmm) REVERT: B 470 ARG cc_start: 0.7864 (mmt180) cc_final: 0.7280 (mmm-85) REVERT: B 480 GLU cc_start: 0.8729 (pm20) cc_final: 0.8336 (pm20) REVERT: B 519 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8024 (pmm) REVERT: B 546 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: B 644 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8011 (ptp90) REVERT: B 667 GLN cc_start: 0.7827 (mt0) cc_final: 0.7356 (mp10) REVERT: A 531 ASN cc_start: 0.7451 (t0) cc_final: 0.6967 (t0) REVERT: A 592 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7350 (mm110) REVERT: A 626 MET cc_start: 0.8262 (mmm) cc_final: 0.7855 (mmp) outliers start: 48 outliers final: 42 residues processed: 138 average time/residue: 0.0985 time to fit residues: 19.4486 Evaluate side-chains 138 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.133161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.113499 restraints weight = 50355.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.115849 restraints weight = 34947.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.117310 restraints weight = 26713.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.117831 restraints weight = 22066.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.118942 restraints weight = 19752.571| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10138 Z= 0.152 Angle : 0.724 12.305 13735 Z= 0.353 Chirality : 0.043 0.193 1535 Planarity : 0.005 0.065 1771 Dihedral : 4.378 20.037 1349 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.47 % Allowed : 25.75 % Favored : 69.77 % 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 are not related in a simple way. whole: -0.45 (0.24), residues: 1239 helix: 0.70 (0.20), residues: 666 sheet: -1.72 (0.48), residues: 102 loop : -1.35 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 571 TYR 0.015 0.001 TYR A 638 PHE 0.027 0.002 PHE A 539 TRP 0.027 0.002 TRP B 305 HIS 0.011 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10138) covalent geometry : angle 0.72435 / 0.35 (13735) hydrogen bonds : bond 0.03855 / 2.46 ( 508) hydrogen bonds : angle 5.03170 / 3.61 ( 1485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 429 MET cc_start: 0.5772 (mmm) cc_final: 0.5166 (mmm) REVERT: B 470 ARG cc_start: 0.7940 (mmt180) cc_final: 0.7282 (mmm-85) REVERT: B 480 GLU cc_start: 0.8699 (pm20) cc_final: 0.8312 (pm20) REVERT: B 519 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8041 (pmm) REVERT: B 546 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: B 582 LYS cc_start: 0.8565 (tmtt) cc_final: 0.8319 (tmtt) REVERT: B 644 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7849 (ptp90) REVERT: B 667 GLN cc_start: 0.7841 (mt0) cc_final: 0.7324 (mp10) REVERT: A 531 ASN cc_start: 0.7545 (t0) cc_final: 0.7100 (t0) REVERT: A 592 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7399 (mm110) REVERT: A 626 MET cc_start: 0.8283 (mmm) cc_final: 0.7895 (mmp) outliers start: 49 outliers final: 42 residues processed: 136 average time/residue: 0.0922 time to fit residues: 18.0868 Evaluate side-chains 136 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 91 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 HIS ** B 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 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 = 0.4598 r_free = 0.4598 target = 0.130985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.110813 restraints weight = 51394.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.113201 restraints weight = 35359.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.114877 restraints weight = 26816.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.115434 restraints weight = 21771.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.116504 restraints weight = 19416.591| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10138 Z= 0.189 Angle : 0.759 11.542 13735 Z= 0.377 Chirality : 0.044 0.233 1535 Planarity : 0.006 0.071 1771 Dihedral : 4.497 20.625 1349 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.66 % Allowed : 25.75 % Favored : 69.59 % 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 are not related in a simple way. whole: -0.62 (0.24), residues: 1239 helix: 0.54 (0.20), residues: 666 sheet: -1.63 (0.50), residues: 96 loop : -1.44 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 571 TYR 0.015 0.002 TYR A 396 PHE 0.027 0.002 PHE A 539 TRP 0.028 0.002 TRP B 305 HIS 0.010 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (10138) covalent geometry : angle 0.75897 / 0.38 (13735) hydrogen bonds : bond 0.04226 / 2.68 ( 508) hydrogen bonds : angle 5.18731 / 3.73 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1742.66 seconds wall clock time: 31 minutes 3.28 seconds (1863.28 seconds total)