Starting phenix.real_space_refine on Sat Aug 23 01:24:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy3_29551/08_2025/8fy3_29551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy3_29551/08_2025/8fy3_29551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fy3_29551/08_2025/8fy3_29551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy3_29551/08_2025/8fy3_29551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fy3_29551/08_2025/8fy3_29551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy3_29551/08_2025/8fy3_29551.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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 55 5.16 5 C 5739 2.51 5 N 1537 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4520 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 25, 'TRANS': 535} Chain breaks: 6 Chain: "B" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4114 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 504} Chain breaks: 6 Chain: "C" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 7, 'TRANS': 30} Time building chain proxies: 2.66, per 1000 atoms: 0.30 Number of scatterers: 8948 At special positions: 0 Unit cell: (69.3, 107.415, 178.101, 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 55 16.00 O 1617 8.00 N 1537 7.00 C 5739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 283.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 71.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 24 through 40 Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.669A pdb=" N HIS A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 82 removed outlier: 3.760A pdb=" N ILE A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.188A pdb=" N VAL A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 163 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.525A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.705A pdb=" N VAL A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.986A pdb=" N LEU A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.517A pdb=" N VAL A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.045A pdb=" N TRP A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.761A pdb=" N ILE A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.925A pdb=" N PHE A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.641A pdb=" N HIS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 496 through 511 Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.789A pdb=" N ILE A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 removed outlier: 3.786A pdb=" N MET A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 557 through 567 Processing helix chain 'A' and resid 579 through 592 removed outlier: 4.615A pdb=" N ILE A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.767A pdb=" N TRP A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 60 through 75 removed outlier: 4.018A pdb=" N ILE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 164 through 181 Processing helix chain 'B' and resid 208 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.509A pdb=" N SER B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 308 through 331 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 370 through 382 removed outlier: 3.757A pdb=" N GLU B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 403 removed outlier: 3.686A pdb=" N ASN B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.633A pdb=" N ILE B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 547 Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 566 through 584 Processing helix chain 'B' and resid 586 through 594 removed outlier: 3.595A pdb=" N THR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.670A pdb=" N ALA B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 672 removed outlier: 3.518A pdb=" N LYS B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.551A pdb=" N ILE B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1575 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: 1.47 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2912 1.34 - 1.46: 1860 1.46 - 1.58: 4286 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 9137 Sorted by residual: bond pdb=" CA PRO B 679 " pdb=" C PRO B 679 " ideal model delta sigma weight residual 1.514 1.520 -0.005 5.50e-03 3.31e+04 9.83e-01 bond pdb=" N TYR B 634 " pdb=" CA TYR B 634 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.80e-01 bond pdb=" C TYR B 634 " pdb=" N PRO B 635 " ideal model delta sigma weight residual 1.340 1.364 -0.023 2.76e-02 1.31e+03 7.25e-01 bond pdb=" CB PRO B 635 " pdb=" CG PRO B 635 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.13e-01 bond pdb=" CG GLU A 261 " pdb=" CD GLU A 261 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.65e-01 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12238 2.05 - 4.10: 103 4.10 - 6.15: 14 6.15 - 8.19: 1 8.19 - 10.24: 1 Bond angle restraints: 12357 Sorted by residual: angle pdb=" CA TRP C 312 " pdb=" CB TRP C 312 " pdb=" CG TRP C 312 " ideal model delta sigma weight residual 113.60 118.72 -5.12 1.90e+00 2.77e-01 7.27e+00 angle pdb=" C LYS A 23 " pdb=" N ASN A 24 " pdb=" CA ASN A 24 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.87e+00 angle pdb=" C ILE C 310 " pdb=" N GLN C 311 " pdb=" CA GLN C 311 " ideal model delta sigma weight residual 122.39 119.18 3.21 1.64e+00 3.72e-01 3.83e+00 angle pdb=" CA LEU A 240 " pdb=" CB LEU A 240 " pdb=" CG LEU A 240 " ideal model delta sigma weight residual 116.30 122.89 -6.59 3.50e+00 8.16e-02 3.54e+00 angle pdb=" CA ARG B 84 " pdb=" CB ARG B 84 " pdb=" CG ARG B 84 " ideal model delta sigma weight residual 114.10 117.86 -3.76 2.00e+00 2.50e-01 3.53e+00 ... (remaining 12352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5187 17.23 - 34.45: 272 34.45 - 51.68: 62 51.68 - 68.91: 13 68.91 - 86.13: 3 Dihedral angle restraints: 5537 sinusoidal: 2236 harmonic: 3301 Sorted by residual: dihedral pdb=" CA SER B 241 " pdb=" C SER B 241 " pdb=" N VAL B 242 " pdb=" CA VAL B 242 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLN C 311 " pdb=" C GLN C 311 " pdb=" N TRP C 312 " pdb=" CA TRP C 312 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB ARG A 211 " pdb=" CG ARG A 211 " pdb=" CD ARG A 211 " pdb=" NE ARG A 211 " ideal model delta sinusoidal sigma weight residual -180.00 -121.12 -58.88 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 797 0.027 - 0.053: 401 0.053 - 0.080: 141 0.080 - 0.107: 50 0.107 - 0.133: 4 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ILE C 310 " pdb=" N ILE C 310 " pdb=" C ILE C 310 " pdb=" CB ILE C 310 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 453 " pdb=" N ILE B 453 " pdb=" C ILE B 453 " pdb=" CB ILE B 453 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CB PRO A 154 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 1390 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 475 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 476 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 240 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 241 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 312 " -0.013 2.00e-02 2.50e+03 8.38e-03 1.75e+00 pdb=" CG TRP C 312 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 312 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 312 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 312 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 312 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 312 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 312 " -0.001 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 400 2.73 - 3.27: 9333 3.27 - 3.81: 15008 3.81 - 4.36: 17488 4.36 - 4.90: 30067 Nonbonded interactions: 72296 Sorted by model distance: nonbonded pdb=" O ILE A 368 " pdb=" OG SER A 407 " model vdw 2.186 3.040 nonbonded pdb=" O SER B 75 " pdb=" OG1 THR B 78 " model vdw 2.187 3.040 nonbonded pdb=" NE2 GLN A 102 " pdb=" OG SER A 104 " model vdw 2.222 3.120 nonbonded pdb=" O LEU B 158 " pdb=" OG1 THR B 162 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A 138 " pdb=" OD1 ASP A 140 " model vdw 2.229 3.040 ... (remaining 72291 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.050 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:9.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9137 Z= 0.135 Angle : 0.492 10.243 12357 Z= 0.255 Chirality : 0.036 0.133 1393 Planarity : 0.004 0.041 1577 Dihedral : 11.506 86.133 3383 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.96 % Allowed : 6.33 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1093 helix: 1.55 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -1.31 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 238 TYR 0.013 0.001 TYR B 261 PHE 0.012 0.002 PHE B 571 TRP 0.023 0.002 TRP C 312 HIS 0.003 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9137) covalent geometry : angle 0.49196 (12357) hydrogen bonds : bond 0.13095 ( 533) hydrogen bonds : angle 4.63481 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.351 Fit side-chains REVERT: A 73 PHE cc_start: 0.7729 (t80) cc_final: 0.7143 (t80) REVERT: A 547 MET cc_start: 0.2744 (mmt) cc_final: 0.2518 (mmt) REVERT: A 617 MET cc_start: 0.4735 (pmm) cc_final: 0.2549 (ttm) REVERT: B 73 PHE cc_start: 0.7544 (m-10) cc_final: 0.7328 (m-10) REVERT: B 135 LYS cc_start: 0.6496 (mtmt) cc_final: 0.5714 (ttpp) REVERT: B 292 ARG cc_start: 0.7206 (mtt90) cc_final: 0.6476 (mtp85) REVERT: B 322 GLU cc_start: 0.7040 (tp30) cc_final: 0.6713 (tp30) REVERT: B 331 SER cc_start: 0.7306 (t) cc_final: 0.7078 (p) REVERT: B 344 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7933 (ttm170) REVERT: B 347 CYS cc_start: 0.8111 (m) cc_final: 0.7678 (p) REVERT: B 370 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7265 (mtt-85) REVERT: B 525 LYS cc_start: 0.7238 (tttp) cc_final: 0.6416 (pmtt) REVERT: B 575 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7535 (mp) outliers start: 29 outliers final: 6 residues processed: 192 average time/residue: 0.5805 time to fit residues: 119.3902 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 575 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 125 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 410 GLN B 95 HIS ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.269150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.217715 restraints weight = 8502.653| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 2.73 r_work: 0.4045 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9137 Z= 0.136 Angle : 0.542 10.471 12357 Z= 0.268 Chirality : 0.037 0.136 1393 Planarity : 0.004 0.060 1577 Dihedral : 4.954 54.827 1207 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.58 % Allowed : 11.34 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1093 helix: 1.59 (0.19), residues: 781 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 390 TYR 0.010 0.001 TYR B 163 PHE 0.015 0.002 PHE A 68 TRP 0.017 0.002 TRP C 312 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9137) covalent geometry : angle 0.54185 (12357) hydrogen bonds : bond 0.03898 ( 533) hydrogen bonds : angle 3.88794 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.401 Fit side-chains REVERT: A 42 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: A 73 PHE cc_start: 0.7122 (t80) cc_final: 0.6692 (t80) REVERT: A 362 ASP cc_start: 0.6264 (m-30) cc_final: 0.5195 (p0) REVERT: A 617 MET cc_start: 0.4540 (pmm) cc_final: 0.4337 (pmm) REVERT: B 135 LYS cc_start: 0.7008 (mtmt) cc_final: 0.6415 (ttpp) REVERT: B 285 MET cc_start: 0.8359 (tpt) cc_final: 0.8157 (mmm) REVERT: B 344 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7731 (ttm170) REVERT: B 347 CYS cc_start: 0.8354 (m) cc_final: 0.7906 (p) REVERT: B 525 LYS cc_start: 0.7140 (tttp) cc_final: 0.6342 (pmtt) REVERT: B 558 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6953 (ttpm) REVERT: C 293 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7576 (mp) outliers start: 35 outliers final: 11 residues processed: 131 average time/residue: 0.4574 time to fit residues: 65.1043 Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 0.0050 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN B 85 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.265064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.204180 restraints weight = 8497.528| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.16 r_work: 0.4031 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9137 Z= 0.185 Angle : 0.584 11.149 12357 Z= 0.284 Chirality : 0.039 0.138 1393 Planarity : 0.004 0.065 1577 Dihedral : 4.441 56.892 1201 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.37 % Allowed : 13.18 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1093 helix: 1.45 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 390 TYR 0.014 0.001 TYR B 163 PHE 0.015 0.002 PHE B 304 TRP 0.020 0.002 TRP C 312 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9137) covalent geometry : angle 0.58414 (12357) hydrogen bonds : bond 0.03995 ( 533) hydrogen bonds : angle 3.92230 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8065 (tp30) cc_final: 0.7799 (tm-30) REVERT: A 73 PHE cc_start: 0.7113 (t80) cc_final: 0.6728 (t80) REVERT: A 362 ASP cc_start: 0.6291 (m-30) cc_final: 0.6065 (t0) REVERT: A 617 MET cc_start: 0.4538 (pmm) cc_final: 0.2820 (ttm) REVERT: B 135 LYS cc_start: 0.7157 (mtmt) cc_final: 0.6480 (ttpp) REVERT: B 347 CYS cc_start: 0.8413 (m) cc_final: 0.7942 (p) REVERT: B 525 LYS cc_start: 0.7283 (tttp) cc_final: 0.6291 (pmtt) REVERT: B 558 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7253 (ttpt) REVERT: C 293 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7690 (mp) outliers start: 33 outliers final: 15 residues processed: 124 average time/residue: 0.3819 time to fit residues: 51.4428 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.266549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.205809 restraints weight = 8614.345| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.20 r_work: 0.4064 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9137 Z= 0.124 Angle : 0.511 10.378 12357 Z= 0.253 Chirality : 0.037 0.130 1393 Planarity : 0.004 0.058 1577 Dihedral : 4.309 57.724 1201 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.06 % Allowed : 13.99 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.26), residues: 1093 helix: 1.62 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.06 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 390 TYR 0.010 0.001 TYR B 355 PHE 0.013 0.001 PHE A 196 TRP 0.018 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9137) covalent geometry : angle 0.51087 (12357) hydrogen bonds : bond 0.03561 ( 533) hydrogen bonds : angle 3.70664 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8023 (tp30) cc_final: 0.7723 (tm-30) REVERT: A 42 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: A 73 PHE cc_start: 0.7168 (t80) cc_final: 0.6658 (t80) REVERT: A 617 MET cc_start: 0.4492 (pmm) cc_final: 0.2673 (ttm) REVERT: B 135 LYS cc_start: 0.7099 (mtmt) cc_final: 0.6441 (ttpp) REVERT: B 347 CYS cc_start: 0.8377 (m) cc_final: 0.7918 (p) REVERT: B 525 LYS cc_start: 0.7299 (tttp) cc_final: 0.6357 (pmtt) REVERT: B 558 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7212 (ttpt) REVERT: C 293 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7653 (mp) outliers start: 30 outliers final: 13 residues processed: 129 average time/residue: 0.3875 time to fit residues: 54.2006 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.0010 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.267499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.206976 restraints weight = 8548.413| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.19 r_work: 0.4083 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9137 Z= 0.118 Angle : 0.503 9.793 12357 Z= 0.248 Chirality : 0.036 0.132 1393 Planarity : 0.004 0.055 1577 Dihedral : 4.213 57.684 1201 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.17 % Allowed : 14.40 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.26), residues: 1093 helix: 1.75 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -1.04 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.013 0.001 TYR B 163 PHE 0.014 0.001 PHE A 196 TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9137) covalent geometry : angle 0.50304 (12357) hydrogen bonds : bond 0.03422 ( 533) hydrogen bonds : angle 3.61110 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8004 (tp30) cc_final: 0.7773 (tm-30) REVERT: A 33 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7254 (tp-100) REVERT: A 34 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6575 (t-90) REVERT: A 37 ASN cc_start: 0.6754 (p0) cc_final: 0.6352 (p0) REVERT: A 42 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: A 73 PHE cc_start: 0.7209 (t80) cc_final: 0.6785 (t80) REVERT: A 362 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.4972 (p0) REVERT: A 617 MET cc_start: 0.4511 (pmm) cc_final: 0.2691 (ttm) REVERT: B 135 LYS cc_start: 0.7063 (mtmt) cc_final: 0.6369 (ttpp) REVERT: B 347 CYS cc_start: 0.8348 (m) cc_final: 0.7894 (p) REVERT: B 525 LYS cc_start: 0.7280 (tttp) cc_final: 0.6375 (pmtt) REVERT: B 531 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7275 (tt) REVERT: B 558 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7136 (ttpt) REVERT: B 575 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 293 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7589 (mp) outliers start: 31 outliers final: 13 residues processed: 126 average time/residue: 0.4186 time to fit residues: 57.4194 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.267684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.207117 restraints weight = 8518.605| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.19 r_work: 0.4069 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9137 Z= 0.117 Angle : 0.490 7.050 12357 Z= 0.244 Chirality : 0.036 0.129 1393 Planarity : 0.004 0.053 1577 Dihedral : 3.840 22.504 1199 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.39 % Allowed : 13.59 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.26), residues: 1093 helix: 1.82 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.010 0.001 TYR B 355 PHE 0.014 0.001 PHE A 196 TRP 0.016 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9137) covalent geometry : angle 0.48965 (12357) hydrogen bonds : bond 0.03328 ( 533) hydrogen bonds : angle 3.54000 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.409 Fit side-chains REVERT: A 33 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7534 (tm-30) REVERT: A 34 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6518 (t-90) REVERT: A 37 ASN cc_start: 0.6777 (p0) cc_final: 0.6515 (p0) REVERT: A 42 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: A 73 PHE cc_start: 0.7265 (t80) cc_final: 0.6871 (t80) REVERT: A 77 GLU cc_start: 0.7264 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 414 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7609 (pt) REVERT: A 617 MET cc_start: 0.4468 (pmm) cc_final: 0.2578 (ttm) REVERT: B 135 LYS cc_start: 0.7100 (mtmt) cc_final: 0.6445 (ttpp) REVERT: B 344 ARG cc_start: 0.8048 (tmm-80) cc_final: 0.7777 (ttm170) REVERT: B 347 CYS cc_start: 0.8385 (m) cc_final: 0.7949 (p) REVERT: B 525 LYS cc_start: 0.7310 (tttp) cc_final: 0.6413 (pmtt) REVERT: B 531 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7322 (tt) REVERT: B 558 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7145 (ttpt) REVERT: B 575 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7669 (mp) REVERT: C 293 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7610 (mp) outliers start: 43 outliers final: 17 residues processed: 136 average time/residue: 0.4702 time to fit residues: 69.5097 Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.265960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.204738 restraints weight = 8535.673| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.20 r_work: 0.4036 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9137 Z= 0.142 Angle : 0.530 7.958 12357 Z= 0.260 Chirality : 0.037 0.130 1393 Planarity : 0.004 0.056 1577 Dihedral : 3.898 23.099 1199 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.27 % Allowed : 15.02 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.26), residues: 1093 helix: 1.80 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.012 0.001 TYR B 355 PHE 0.014 0.002 PHE A 196 TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9137) covalent geometry : angle 0.52954 (12357) hydrogen bonds : bond 0.03489 ( 533) hydrogen bonds : angle 3.58193 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.345 Fit side-chains REVERT: A 33 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7385 (tm-30) REVERT: A 34 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6511 (t-90) REVERT: A 37 ASN cc_start: 0.6709 (p0) cc_final: 0.6430 (p0) REVERT: A 42 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: A 73 PHE cc_start: 0.7242 (t80) cc_final: 0.6794 (t80) REVERT: A 77 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 362 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.6067 (t0) REVERT: A 617 MET cc_start: 0.4491 (pmm) cc_final: 0.2654 (ttm) REVERT: B 344 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7792 (ttm170) REVERT: B 347 CYS cc_start: 0.8392 (m) cc_final: 0.7956 (p) REVERT: B 525 LYS cc_start: 0.7337 (tttp) cc_final: 0.6376 (pmtt) REVERT: C 293 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7628 (mp) outliers start: 32 outliers final: 15 residues processed: 126 average time/residue: 0.4342 time to fit residues: 59.1844 Evaluate side-chains 122 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.267659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.207100 restraints weight = 8542.720| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.21 r_work: 0.4080 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9137 Z= 0.116 Angle : 0.506 7.564 12357 Z= 0.250 Chirality : 0.036 0.127 1393 Planarity : 0.004 0.053 1577 Dihedral : 3.830 21.873 1199 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.96 % Allowed : 15.53 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.26), residues: 1093 helix: 1.91 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.010 0.001 TYR B 355 PHE 0.012 0.001 PHE A 196 TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9137) covalent geometry : angle 0.50593 (12357) hydrogen bonds : bond 0.03291 ( 533) hydrogen bonds : angle 3.51717 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.227 Fit side-chains REVERT: A 33 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7257 (tm-30) REVERT: A 34 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.6429 (t-90) REVERT: A 37 ASN cc_start: 0.6619 (p0) cc_final: 0.6295 (p0) REVERT: A 42 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: A 73 PHE cc_start: 0.7185 (t80) cc_final: 0.6706 (t80) REVERT: A 77 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7049 (mm-30) REVERT: A 126 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6893 (mm-30) REVERT: A 617 MET cc_start: 0.4539 (pmm) cc_final: 0.2660 (ttm) REVERT: B 135 LYS cc_start: 0.7051 (mtmt) cc_final: 0.6377 (ttpp) REVERT: B 243 MET cc_start: 0.5373 (mtm) cc_final: 0.5102 (mtp) REVERT: B 344 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7700 (ttm170) REVERT: B 347 CYS cc_start: 0.8378 (m) cc_final: 0.7902 (p) REVERT: B 525 LYS cc_start: 0.7314 (tttp) cc_final: 0.6380 (pmtt) REVERT: C 293 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7548 (mp) outliers start: 29 outliers final: 13 residues processed: 121 average time/residue: 0.4816 time to fit residues: 63.1262 Evaluate side-chains 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN B 149 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.267286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.206797 restraints weight = 8541.800| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.19 r_work: 0.4067 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9137 Z= 0.121 Angle : 0.516 7.640 12357 Z= 0.255 Chirality : 0.036 0.128 1393 Planarity : 0.004 0.053 1577 Dihedral : 3.825 22.221 1199 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.35 % Allowed : 16.24 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.26), residues: 1093 helix: 1.92 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.88 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.011 0.001 TYR B 355 PHE 0.012 0.001 PHE A 196 TRP 0.016 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9137) covalent geometry : angle 0.51569 (12357) hydrogen bonds : bond 0.03294 ( 533) hydrogen bonds : angle 3.52181 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.362 Fit side-chains REVERT: A 33 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7350 (tm-30) REVERT: A 34 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6371 (t-90) REVERT: A 37 ASN cc_start: 0.6661 (p0) cc_final: 0.6425 (p0) REVERT: A 73 PHE cc_start: 0.7237 (t80) cc_final: 0.6752 (t80) REVERT: A 77 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7123 (mm-30) REVERT: A 162 ASP cc_start: 0.7592 (m-30) cc_final: 0.7328 (m-30) REVERT: A 414 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7421 (pt) REVERT: A 617 MET cc_start: 0.4572 (pmm) cc_final: 0.2753 (ttm) REVERT: B 243 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.5181 (mtp) REVERT: B 344 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7715 (ttm170) REVERT: B 347 CYS cc_start: 0.8380 (m) cc_final: 0.7937 (p) REVERT: B 525 LYS cc_start: 0.7297 (tttp) cc_final: 0.6373 (pmtt) REVERT: B 561 GLN cc_start: 0.7544 (mp10) cc_final: 0.7305 (mm-40) REVERT: C 293 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7581 (mp) outliers start: 23 outliers final: 13 residues processed: 118 average time/residue: 0.4708 time to fit residues: 60.3757 Evaluate side-chains 116 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 0.0970 chunk 51 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.0070 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.264819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.203461 restraints weight = 8516.931| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.19 r_work: 0.4029 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9137 Z= 0.160 Angle : 0.557 8.191 12357 Z= 0.274 Chirality : 0.038 0.132 1393 Planarity : 0.004 0.059 1577 Dihedral : 3.963 22.972 1199 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.15 % Allowed : 16.55 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.26), residues: 1093 helix: 1.75 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.013 0.001 TYR B 355 PHE 0.015 0.002 PHE A 196 TRP 0.019 0.001 TRP C 312 HIS 0.005 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9137) covalent geometry : angle 0.55660 (12357) hydrogen bonds : bond 0.03576 ( 533) hydrogen bonds : angle 3.62475 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.355 Fit side-chains REVERT: A 33 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7313 (tm-30) REVERT: A 34 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6430 (t-90) REVERT: A 37 ASN cc_start: 0.6713 (p0) cc_final: 0.6440 (p0) REVERT: A 42 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7043 (tp30) REVERT: A 73 PHE cc_start: 0.7231 (t80) cc_final: 0.6745 (t80) REVERT: A 77 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7134 (mm-30) REVERT: A 414 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7319 (pt) REVERT: B 243 MET cc_start: 0.5561 (OUTLIER) cc_final: 0.5237 (mtp) REVERT: B 344 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7792 (ttm170) REVERT: B 347 CYS cc_start: 0.8425 (m) cc_final: 0.7960 (p) REVERT: B 525 LYS cc_start: 0.7282 (tttp) cc_final: 0.6305 (pmtt) REVERT: B 561 GLN cc_start: 0.7647 (mp10) cc_final: 0.7379 (mm-40) REVERT: C 293 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7688 (mp) outliers start: 21 outliers final: 13 residues processed: 117 average time/residue: 0.5225 time to fit residues: 66.1933 Evaluate side-chains 119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 94 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 110 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.267108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.206743 restraints weight = 8486.999| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.19 r_work: 0.4067 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9137 Z= 0.119 Angle : 0.526 7.779 12357 Z= 0.260 Chirality : 0.036 0.127 1393 Planarity : 0.004 0.054 1577 Dihedral : 3.878 21.503 1199 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.94 % Allowed : 17.06 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.26), residues: 1093 helix: 1.88 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.009 0.001 TYR B 355 PHE 0.012 0.001 PHE A 196 TRP 0.016 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9137) covalent geometry : angle 0.52551 (12357) hydrogen bonds : bond 0.03324 ( 533) hydrogen bonds : angle 3.55192 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3906.35 seconds wall clock time: 67 minutes 15.44 seconds (4035.44 seconds total)