Starting phenix.real_space_refine on Thu Mar 13 14:01:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy3_29551/03_2025/8fy3_29551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy3_29551/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fy3_29551/03_2025/8fy3_29551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy3_29551/03_2025/8fy3_29551.map" model { file = "/net/cci-nas-00/data/ceres_data/8fy3_29551/03_2025/8fy3_29551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy3_29551/03_2025/8fy3_29551.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.05, per 1000 atoms: 0.68 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.78 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: 2.39 Time building geometry restraints manager: 2.71 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: 3.490 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: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.870 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- 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= 0.202 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (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 TRP 0.023 0.002 TRP C 312 HIS 0.003 0.001 HIS B 303 PHE 0.012 0.002 PHE B 571 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG A 238 *********************** 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 : 0.995 Fit side-chains REVERT: A 73 PHE cc_start: 0.7729 (t80) cc_final: 0.7143 (t80) REVERT: A 360 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6534 (tm-30) 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: 0.7079 (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: 0.7264 (mtt-85) REVERT: B 525 LYS cc_start: 0.7238 (tttp) cc_final: 0.6417 (pmtt) REVERT: B 575 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7534 (mp) outliers start: 29 outliers final: 6 residues processed: 192 average time/residue: 1.1131 time to fit residues: 229.6230 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 : 1.000 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 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 85 GLN B 95 HIS ** B 352 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 = 0.4825 r_free = 0.4825 target = 0.266685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.206995 restraints weight = 8418.904| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.16 r_work: 0.4080 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9137 Z= 0.265 Angle : 0.575 10.921 12357 Z= 0.283 Chirality : 0.039 0.138 1393 Planarity : 0.004 0.065 1577 Dihedral : 5.063 55.480 1207 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.88 % Allowed : 11.24 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1093 helix: 1.46 (0.19), residues: 781 sheet: None (None), residues: 0 loop : -1.22 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 312 HIS 0.005 0.001 HIS C 292 PHE 0.014 0.002 PHE A 206 TYR 0.011 0.001 TYR B 355 ARG 0.011 0.000 ARG B 390 *********************** 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 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.895 Fit side-chains REVERT: A 42 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: A 360 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6003 (tm-30) REVERT: A 362 ASP cc_start: 0.6302 (m-30) cc_final: 0.5202 (p0) REVERT: A 617 MET cc_start: 0.4540 (pmm) cc_final: 0.4336 (pmm) REVERT: B 135 LYS cc_start: 0.7066 (mtmt) cc_final: 0.6443 (ttpp) REVERT: B 344 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7813 (ttm170) REVERT: B 347 CYS cc_start: 0.8413 (m) cc_final: 0.7959 (p) REVERT: B 525 LYS cc_start: 0.7267 (tttp) cc_final: 0.6372 (pmtt) REVERT: B 558 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7048 (ttpm) REVERT: C 293 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7637 (mp) outliers start: 38 outliers final: 13 residues processed: 134 average time/residue: 0.9835 time to fit residues: 143.5829 Evaluate side-chains 112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 278 VAL 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 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 93 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 61 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 125 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4842 r_free = 0.4842 target = 0.268950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.209672 restraints weight = 8555.174| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.20 r_work: 0.4096 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9137 Z= 0.162 Angle : 0.505 10.240 12357 Z= 0.248 Chirality : 0.036 0.131 1393 Planarity : 0.004 0.055 1577 Dihedral : 4.553 54.626 1203 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.58 % Allowed : 12.87 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1093 helix: 1.65 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.20 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 312 HIS 0.003 0.001 HIS A 39 PHE 0.012 0.001 PHE A 196 TYR 0.010 0.001 TYR B 163 ARG 0.005 0.000 ARG B 390 *********************** 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 142 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8030 (tp30) cc_final: 0.7771 (tm-30) REVERT: A 42 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6906 (tp30) REVERT: A 73 PHE cc_start: 0.7577 (t80) cc_final: 0.7078 (t80) REVERT: A 77 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7023 (mm-30) REVERT: A 362 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5058 (p0) REVERT: A 617 MET cc_start: 0.4529 (pmm) cc_final: 0.2743 (ttm) REVERT: B 135 LYS cc_start: 0.6964 (mtmt) cc_final: 0.6300 (ttpp) REVERT: B 344 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7726 (ttm170) REVERT: B 347 CYS cc_start: 0.8401 (m) cc_final: 0.7917 (p) REVERT: B 525 LYS cc_start: 0.7229 (tttp) cc_final: 0.6384 (pmtt) REVERT: B 531 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7096 (tt) REVERT: B 558 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7160 (ttpt) REVERT: C 293 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7572 (mp) outliers start: 35 outliers final: 10 residues processed: 127 average time/residue: 1.1459 time to fit residues: 157.5849 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 531 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.266709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.205994 restraints weight = 8480.072| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.18 r_work: 0.4052 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9137 Z= 0.224 Angle : 0.526 10.639 12357 Z= 0.259 Chirality : 0.037 0.134 1393 Planarity : 0.004 0.057 1577 Dihedral : 4.248 55.187 1201 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.37 % Allowed : 13.79 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1093 helix: 1.64 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.07 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.008 0.001 HIS B 219 PHE 0.013 0.002 PHE A 196 TYR 0.012 0.001 TYR B 163 ARG 0.004 0.000 ARG B 390 *********************** 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 134 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: A 77 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6463 (mm-30) REVERT: A 362 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.5169 (p0) REVERT: A 414 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7643 (pt) REVERT: A 617 MET cc_start: 0.4483 (pmm) cc_final: 0.2667 (ttm) REVERT: B 135 LYS cc_start: 0.7071 (mtmt) cc_final: 0.6430 (ttpp) REVERT: B 347 CYS cc_start: 0.8363 (m) cc_final: 0.7929 (p) REVERT: B 525 LYS cc_start: 0.7322 (tttp) cc_final: 0.6393 (pmtt) REVERT: B 558 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7238 (ttpt) REVERT: B 575 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7709 (mp) REVERT: C 293 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7628 (mp) outliers start: 33 outliers final: 13 residues processed: 123 average time/residue: 0.9631 time to fit residues: 128.8395 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN 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 362 ASP Chi-restraints excluded: chain A residue 406 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 107 optimal weight: 0.0040 chunk 82 optimal weight: 0.5980 overall best weight: 0.3910 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.268897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.209140 restraints weight = 8488.172| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.17 r_work: 0.4104 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9137 Z= 0.156 Angle : 0.486 9.709 12357 Z= 0.242 Chirality : 0.036 0.129 1393 Planarity : 0.004 0.051 1577 Dihedral : 4.112 55.314 1201 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.47 % Allowed : 14.71 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1093 helix: 1.84 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -1.01 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 312 HIS 0.003 0.001 HIS B 303 PHE 0.014 0.001 PHE A 196 TYR 0.009 0.001 TYR B 355 ARG 0.002 0.000 ARG B 390 *********************** 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 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 33 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7205 (tp-100) REVERT: A 37 ASN cc_start: 0.6765 (p0) cc_final: 0.6360 (p0) REVERT: A 42 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: A 77 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6421 (mm-30) REVERT: A 236 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7357 (mtt) REVERT: A 362 ASP cc_start: 0.6327 (m-30) cc_final: 0.5085 (p0) REVERT: A 617 MET cc_start: 0.4540 (pmm) cc_final: 0.2735 (ttm) REVERT: B 135 LYS cc_start: 0.6954 (mtmt) cc_final: 0.6278 (ttpp) REVERT: B 347 CYS cc_start: 0.8354 (m) cc_final: 0.7890 (p) REVERT: B 525 LYS cc_start: 0.7236 (tttp) cc_final: 0.6341 (pmtt) REVERT: B 531 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7325 (tt) REVERT: B 558 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7165 (ttpt) REVERT: B 575 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7598 (mp) REVERT: C 293 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7522 (mp) outliers start: 34 outliers final: 14 residues processed: 126 average time/residue: 1.0198 time to fit residues: 139.8918 Evaluate side-chains 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN 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 236 MET Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 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 B residue 531 LEU 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 B residue 602 VAL 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 21 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.4832 r_free = 0.4832 target = 0.267206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.206460 restraints weight = 8479.735| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.21 r_work: 0.4068 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2402 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= 0.203 Angle : 0.507 7.300 12357 Z= 0.250 Chirality : 0.037 0.134 1393 Planarity : 0.004 0.053 1577 Dihedral : 4.162 56.004 1201 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.78 % Allowed : 14.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1093 helix: 1.84 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -0.96 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.014 0.001 PHE A 196 TYR 0.011 0.001 TYR B 355 ARG 0.002 0.000 ARG B 390 *********************** 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 143 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.914 Fit side-chains REVERT: A 33 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7531 (tm-30) REVERT: A 37 ASN cc_start: 0.6704 (p0) cc_final: 0.6452 (p0) REVERT: A 42 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: A 77 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7030 (mm-30) REVERT: A 360 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6080 (tm-30) REVERT: A 362 ASP cc_start: 0.6380 (m-30) cc_final: 0.5135 (p0) REVERT: A 617 MET cc_start: 0.4496 (pmm) cc_final: 0.2682 (ttm) REVERT: B 63 ILE cc_start: 0.8087 (mm) cc_final: 0.7850 (mt) REVERT: B 135 LYS cc_start: 0.7078 (mtmt) cc_final: 0.6406 (ttpp) REVERT: B 347 CYS cc_start: 0.8346 (m) cc_final: 0.7882 (p) REVERT: B 525 LYS cc_start: 0.7288 (tttp) cc_final: 0.6338 (pmtt) REVERT: B 558 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7143 (ttpt) REVERT: B 575 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7656 (mp) REVERT: C 293 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7593 (mp) outliers start: 37 outliers final: 14 residues processed: 130 average time/residue: 0.9906 time to fit residues: 140.5667 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER 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 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 84 optimal weight: 0.2980 chunk 108 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 349 ASN ** A 353 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.267981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.207504 restraints weight = 8558.146| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.21 r_work: 0.4085 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9137 Z= 0.180 Angle : 0.498 7.326 12357 Z= 0.248 Chirality : 0.036 0.130 1393 Planarity : 0.004 0.052 1577 Dihedral : 4.132 56.247 1201 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.86 % Allowed : 15.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1093 helix: 1.92 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.92 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.012 0.001 PHE A 196 TYR 0.010 0.001 TYR B 355 ARG 0.003 0.000 ARG A 397 *********************** 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 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.889 Fit side-chains REVERT: A 33 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7531 (tm-30) REVERT: A 34 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6498 (t-90) REVERT: A 37 ASN cc_start: 0.6743 (p0) cc_final: 0.6496 (p0) REVERT: A 42 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: A 77 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7001 (mm-30) REVERT: A 126 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6885 (mm-30) REVERT: A 360 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6061 (tm-30) REVERT: A 362 ASP cc_start: 0.6550 (m-30) cc_final: 0.6067 (t0) REVERT: A 617 MET cc_start: 0.4483 (pmm) cc_final: 0.2672 (ttm) REVERT: B 63 ILE cc_start: 0.8058 (mm) cc_final: 0.7807 (mt) REVERT: B 135 LYS cc_start: 0.7062 (mtmt) cc_final: 0.6368 (ttpp) REVERT: B 347 CYS cc_start: 0.8390 (m) cc_final: 0.7920 (p) REVERT: B 525 LYS cc_start: 0.7245 (tttp) cc_final: 0.6315 (pmtt) REVERT: B 561 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: C 293 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7555 (mp) outliers start: 28 outliers final: 13 residues processed: 121 average time/residue: 1.0545 time to fit residues: 138.0377 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 : 0.891 ------------------------------------------------------------------------------- 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 261 GLU Chi-restraints excluded: chain A residue 278 VAL 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 561 GLN Chi-restraints excluded: chain B residue 602 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 107 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** 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 = 0.266177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.205066 restraints weight = 8605.601| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.22 r_work: 0.4048 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9137 Z= 0.237 Angle : 0.530 7.656 12357 Z= 0.261 Chirality : 0.037 0.132 1393 Planarity : 0.004 0.057 1577 Dihedral : 3.898 23.153 1199 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.76 % Allowed : 15.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1093 helix: 1.82 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.005 0.001 HIS B 303 PHE 0.014 0.002 PHE B 304 TYR 0.012 0.001 TYR B 355 ARG 0.003 0.000 ARG B 344 *********************** 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 131 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.921 Fit side-chains REVERT: A 33 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7445 (tm-30) REVERT: A 34 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.6519 (t-90) REVERT: A 37 ASN cc_start: 0.6745 (p0) cc_final: 0.6491 (p0) REVERT: A 42 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: A 77 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 126 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6883 (mm-30) REVERT: A 360 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6048 (tm-30) REVERT: A 362 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6228 (t0) REVERT: A 617 MET cc_start: 0.4522 (pmm) cc_final: 0.2774 (ttm) REVERT: B 63 ILE cc_start: 0.8124 (mm) cc_final: 0.7900 (mt) REVERT: B 344 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7795 (ttm170) REVERT: B 347 CYS cc_start: 0.8402 (m) cc_final: 0.7942 (p) REVERT: B 525 LYS cc_start: 0.7302 (tttp) cc_final: 0.6316 (pmtt) REVERT: C 293 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7613 (mp) outliers start: 27 outliers final: 15 residues processed: 122 average time/residue: 1.1729 time to fit residues: 155.5537 Evaluate side-chains 120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 109 ASN 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 602 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 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 80 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 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 100 HIS ** 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** B 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.267441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.206766 restraints weight = 8556.680| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.23 r_work: 0.4070 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9137 Z= 0.190 Angle : 0.508 7.549 12357 Z= 0.252 Chirality : 0.036 0.129 1393 Planarity : 0.004 0.054 1577 Dihedral : 3.829 22.160 1197 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.45 % Allowed : 16.65 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1093 helix: 1.90 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.013 0.001 PHE A 196 TYR 0.010 0.001 TYR B 355 ARG 0.005 0.000 ARG B 344 *********************** 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 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.901 Fit side-chains REVERT: A 33 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7424 (tm-30) REVERT: A 34 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.6517 (t-90) REVERT: A 37 ASN cc_start: 0.6745 (p0) cc_final: 0.6494 (p0) REVERT: A 42 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: A 77 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 232 ARG cc_start: 0.6804 (ptt-90) cc_final: 0.6578 (ptt90) REVERT: A 360 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6081 (tm-30) REVERT: A 362 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6231 (t0) REVERT: A 617 MET cc_start: 0.4557 (pmm) cc_final: 0.2708 (ttm) REVERT: B 63 ILE cc_start: 0.8102 (mm) cc_final: 0.7862 (mt) REVERT: B 135 LYS cc_start: 0.7071 (mtmt) cc_final: 0.6408 (ttpp) REVERT: B 344 ARG cc_start: 0.8037 (tmm-80) cc_final: 0.7738 (ttm170) REVERT: B 347 CYS cc_start: 0.8382 (m) cc_final: 0.7900 (p) REVERT: B 525 LYS cc_start: 0.7288 (tttp) cc_final: 0.6348 (pmtt) REVERT: B 561 GLN cc_start: 0.7560 (mp10) cc_final: 0.7258 (mm-40) REVERT: C 293 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7606 (mp) outliers start: 24 outliers final: 16 residues processed: 118 average time/residue: 1.0346 time to fit residues: 132.0677 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 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 602 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 34 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.0370 chunk 33 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 100 HIS ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 496 HIS ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.268798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.208352 restraints weight = 8565.005| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.23 r_work: 0.4073 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9137 Z= 0.159 Angle : 0.499 7.447 12357 Z= 0.248 Chirality : 0.036 0.126 1393 Planarity : 0.004 0.053 1577 Dihedral : 3.777 21.570 1197 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.04 % Allowed : 16.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.26), residues: 1093 helix: 1.99 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 312 HIS 0.008 0.001 HIS A 100 PHE 0.011 0.001 PHE A 196 TYR 0.016 0.001 TYR A 101 ARG 0.004 0.000 ARG B 344 ********************** 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 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.910 Fit side-chains REVERT: A 33 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7368 (tm-30) REVERT: A 34 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6507 (t-90) REVERT: A 37 ASN cc_start: 0.6699 (p0) cc_final: 0.6446 (p0) REVERT: A 42 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6960 (tp30) REVERT: A 77 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 162 ASP cc_start: 0.7626 (m-30) cc_final: 0.7341 (m-30) REVERT: A 232 ARG cc_start: 0.6787 (ptt-90) cc_final: 0.6556 (ptt90) REVERT: A 360 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6079 (tm-30) REVERT: A 362 ASP cc_start: 0.6449 (m-30) cc_final: 0.6213 (t0) REVERT: A 459 ARG cc_start: 0.5958 (tpp-160) cc_final: 0.5741 (tpm170) REVERT: A 617 MET cc_start: 0.4547 (pmm) cc_final: 0.2635 (ttm) REVERT: B 63 ILE cc_start: 0.8104 (mm) cc_final: 0.7859 (mt) REVERT: B 75 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8273 (t) REVERT: B 135 LYS cc_start: 0.7092 (mtmt) cc_final: 0.6430 (ttpp) REVERT: B 243 MET cc_start: 0.5221 (mtm) cc_final: 0.4996 (mtp) REVERT: B 344 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7716 (ttm170) REVERT: B 347 CYS cc_start: 0.8444 (m) cc_final: 0.7943 (p) REVERT: B 561 GLN cc_start: 0.7608 (mp10) cc_final: 0.7330 (mm-40) REVERT: C 293 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7560 (mp) outliers start: 20 outliers final: 11 residues processed: 119 average time/residue: 1.1658 time to fit residues: 149.6918 Evaluate side-chains 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 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 602 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 101 optimal weight: 0.0040 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 110 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS B 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.268954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.208738 restraints weight = 8549.113| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.22 r_work: 0.4093 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9137 Z= 0.163 Angle : 0.495 7.297 12357 Z= 0.246 Chirality : 0.036 0.126 1393 Planarity : 0.004 0.050 1577 Dihedral : 3.742 21.754 1197 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1093 helix: 2.02 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.86 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.011 0.001 PHE A 196 TYR 0.009 0.001 TYR B 355 ARG 0.004 0.000 ARG B 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8431.79 seconds wall clock time: 147 minutes 8.88 seconds (8828.88 seconds total)