Starting phenix.real_space_refine on Tue Feb 11 17:26:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyo_38779/02_2025/8xyo_38779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyo_38779/02_2025/8xyo_38779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xyo_38779/02_2025/8xyo_38779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyo_38779/02_2025/8xyo_38779.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyo_38779/02_2025/8xyo_38779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyo_38779/02_2025/8xyo_38779.cif" } resolution = 3.04 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= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 4074 2.51 5 N 1047 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6369 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 578, 4729 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 24, 'TRANS': 553} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 578, 4729 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 24, 'TRANS': 553} Chain breaks: 1 bond proxies already assigned to first conformer: 4850 Chain: "B" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.50 Time building chain proxies: 6.77, per 1000 atoms: 1.06 Number of scatterers: 6369 At special positions: 0 Unit cell: (73.95, 93.5, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 1212 8.00 N 1047 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 103 " " NAG A 704 " - " ASN A 53 " " NAG A 705 " - " ASN A 322 " " NAG A 706 " - " ASN A 432 " " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 707 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 374 " 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 58.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.703A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.783A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.919A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.835A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.765A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 4.023A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.611A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 281 removed outlier: 4.162A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.735A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.850A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.686A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.055A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.524A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.882A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.716A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.543A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.156A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.344A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 313 hydrogen bonds defined for protein. 874 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: 1.76 Time building geometry restraints manager: 1.79 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: 2025 1.34 - 1.46: 1534 1.46 - 1.58: 2932 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 6547 Sorted by residual: bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C TYR B 495 " pdb=" N GLY B 496 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 2.13e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C1 NAG A 706 " pdb=" O5 NAG A 706 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 ... (remaining 6542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 8478 1.25 - 2.49: 327 2.49 - 3.74: 71 3.74 - 4.99: 19 4.99 - 6.23: 2 Bond angle restraints: 8897 Sorted by residual: angle pdb=" C THR A 334 " pdb=" N ASP A 335 " pdb=" CA ASP A 335 " ideal model delta sigma weight residual 121.20 125.70 -4.50 1.40e+00 5.10e-01 1.03e+01 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 113.25 116.69 -3.44 1.30e+00 5.92e-01 7.02e+00 angle pdb=" C PRO A 84 " pdb=" N LEU A 85 " pdb=" CA LEU A 85 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.06e+00 angle pdb=" C TYR B 495 " pdb=" N GLY B 496 " pdb=" CA GLY B 496 " ideal model delta sigma weight residual 122.29 120.31 1.98 8.90e-01 1.26e+00 4.93e+00 angle pdb=" CA TRP A 165 " pdb=" CB TRP A 165 " pdb=" CG TRP A 165 " ideal model delta sigma weight residual 113.60 117.33 -3.73 1.90e+00 2.77e-01 3.86e+00 ... (remaining 8892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3590 17.79 - 35.57: 271 35.57 - 53.36: 48 53.36 - 71.14: 12 71.14 - 88.93: 14 Dihedral angle restraints: 3935 sinusoidal: 1669 harmonic: 2266 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 173.04 -80.04 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -48.28 -37.72 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.30 -36.30 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 3932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 508 0.028 - 0.056: 292 0.056 - 0.085: 91 0.085 - 0.113: 47 0.113 - 0.141: 11 Chirality restraints: 949 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 946 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 475 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C LYS A 475 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS A 475 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 476 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 473 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C TRP A 473 " 0.026 2.00e-02 2.50e+03 pdb=" O TRP A 473 " -0.010 2.00e-02 2.50e+03 pdb=" N MET A 474 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 335 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 336 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.020 5.00e-02 4.00e+02 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 69 2.66 - 3.22: 5794 3.22 - 3.78: 9374 3.78 - 4.34: 12820 4.34 - 4.90: 21900 Nonbonded interactions: 49957 Sorted by model distance: nonbonded pdb=" CD GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.097 2.460 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.098 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.105 2.230 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.205 3.040 nonbonded pdb=" O ASP A 431 " pdb=" OG1 THR A 434 " model vdw 2.227 3.040 ... (remaining 49952 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=0.50 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6547 Z= 0.274 Angle : 0.593 6.234 8897 Z= 0.320 Chirality : 0.042 0.141 949 Planarity : 0.004 0.037 1141 Dihedral : 13.686 88.931 2471 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.30), residues: 768 helix: 1.20 (0.27), residues: 395 sheet: 0.42 (0.66), residues: 60 loop : -1.05 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 PHE 0.017 0.002 PHE A 512 TYR 0.016 0.001 TYR A 158 ARG 0.003 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7343 (tt0) cc_final: 0.7074 (tt0) REVERT: A 231 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 243 TYR cc_start: 0.7578 (t80) cc_final: 0.7359 (t80) REVERT: A 299 ASP cc_start: 0.8028 (m-30) cc_final: 0.7727 (m-30) REVERT: A 435 GLU cc_start: 0.7294 (mp0) cc_final: 0.6706 (mp0) REVERT: A 491 VAL cc_start: 0.8438 (t) cc_final: 0.8130 (p) REVERT: A 512 PHE cc_start: 0.8588 (t80) cc_final: 0.8384 (t80) REVERT: A 515 TYR cc_start: 0.8382 (m-80) cc_final: 0.7475 (m-80) REVERT: A 564 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7257 (mm-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1880 time to fit residues: 39.6143 Evaluate side-chains 137 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A 524 GLN B 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101199 restraints weight = 19411.621| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.46 r_work: 0.3167 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6547 Z= 0.352 Angle : 0.613 7.144 8897 Z= 0.323 Chirality : 0.046 0.210 949 Planarity : 0.005 0.039 1141 Dihedral : 6.120 55.641 988 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.47 % Allowed : 6.34 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.30), residues: 768 helix: 1.41 (0.27), residues: 383 sheet: 0.28 (0.67), residues: 61 loop : -1.16 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 165 HIS 0.008 0.002 HIS A 401 PHE 0.020 0.002 PHE A 512 TYR 0.016 0.002 TYR A 158 ARG 0.006 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8281 (tttt) cc_final: 0.8065 (tttt) REVERT: A 75 GLU cc_start: 0.7718 (tt0) cc_final: 0.7457 (tt0) REVERT: A 202 TYR cc_start: 0.8480 (t80) cc_final: 0.8093 (t80) REVERT: A 231 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 243 TYR cc_start: 0.7508 (t80) cc_final: 0.7202 (t80) REVERT: A 299 ASP cc_start: 0.7883 (m-30) cc_final: 0.7643 (m-30) REVERT: A 435 GLU cc_start: 0.7375 (mp0) cc_final: 0.6872 (mp0) REVERT: A 474 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7250 (mpp) REVERT: A 491 VAL cc_start: 0.8426 (t) cc_final: 0.8098 (p) REVERT: A 564 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7207 (mm-30) REVERT: B 395 VAL cc_start: 0.8269 (p) cc_final: 0.7983 (t) outliers start: 10 outliers final: 6 residues processed: 155 average time/residue: 0.1788 time to fit residues: 37.4110 Evaluate side-chains 143 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099322 restraints weight = 20640.896| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.72 r_work: 0.3128 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6547 Z= 0.280 Angle : 0.563 5.697 8897 Z= 0.297 Chirality : 0.044 0.231 949 Planarity : 0.005 0.057 1141 Dihedral : 5.475 55.114 988 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.77 % Allowed : 8.70 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.30), residues: 768 helix: 1.47 (0.27), residues: 383 sheet: 0.24 (0.66), residues: 61 loop : -1.10 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.008 0.001 HIS A 401 PHE 0.016 0.002 PHE A 369 TYR 0.016 0.002 TYR A 158 ARG 0.010 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.710 Fit side-chains REVERT: A 74 LYS cc_start: 0.8106 (tttt) cc_final: 0.7877 (tttt) REVERT: A 75 GLU cc_start: 0.7621 (tt0) cc_final: 0.7319 (tt0) REVERT: A 150 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 202 TYR cc_start: 0.8322 (t80) cc_final: 0.7863 (t80) REVERT: A 243 TYR cc_start: 0.7432 (t80) cc_final: 0.7084 (t80) REVERT: A 299 ASP cc_start: 0.7852 (m-30) cc_final: 0.7605 (m-30) REVERT: A 435 GLU cc_start: 0.7356 (mp0) cc_final: 0.6775 (mp0) REVERT: A 491 VAL cc_start: 0.8427 (t) cc_final: 0.8060 (p) REVERT: A 564 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7364 (mm-30) REVERT: B 395 VAL cc_start: 0.8202 (p) cc_final: 0.7915 (t) REVERT: B 451 TYR cc_start: 0.8230 (m-80) cc_final: 0.7903 (m-80) outliers start: 12 outliers final: 8 residues processed: 155 average time/residue: 0.1838 time to fit residues: 37.7855 Evaluate side-chains 153 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100675 restraints weight = 22434.628| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.87 r_work: 0.3135 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6547 Z= 0.194 Angle : 0.516 5.285 8897 Z= 0.273 Chirality : 0.042 0.233 949 Planarity : 0.004 0.046 1141 Dihedral : 4.935 55.467 988 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.06 % Allowed : 10.18 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.30), residues: 768 helix: 1.66 (0.27), residues: 379 sheet: 0.46 (0.68), residues: 59 loop : -1.05 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.006 0.001 HIS A 401 PHE 0.012 0.001 PHE A 369 TYR 0.013 0.001 TYR B 396 ARG 0.017 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.754 Fit side-chains REVERT: A 74 LYS cc_start: 0.8045 (tttt) cc_final: 0.7803 (tttt) REVERT: A 75 GLU cc_start: 0.7607 (tt0) cc_final: 0.7295 (tt0) REVERT: A 202 TYR cc_start: 0.8255 (t80) cc_final: 0.7890 (t80) REVERT: A 243 TYR cc_start: 0.7388 (t80) cc_final: 0.7107 (t80) REVERT: A 299 ASP cc_start: 0.7889 (m-30) cc_final: 0.7635 (m-30) REVERT: A 435 GLU cc_start: 0.7387 (mp0) cc_final: 0.6804 (mp0) REVERT: A 474 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6991 (mpp) REVERT: A 491 VAL cc_start: 0.8386 (t) cc_final: 0.8010 (p) REVERT: A 564 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7207 (mm-30) REVERT: B 395 VAL cc_start: 0.8153 (p) cc_final: 0.7827 (t) REVERT: B 433 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8104 (t) outliers start: 14 outliers final: 7 residues processed: 149 average time/residue: 0.1821 time to fit residues: 36.0743 Evaluate side-chains 146 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099072 restraints weight = 15300.551| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.24 r_work: 0.3141 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6547 Z= 0.356 Angle : 0.587 6.084 8897 Z= 0.309 Chirality : 0.045 0.241 949 Planarity : 0.004 0.040 1141 Dihedral : 5.119 56.136 988 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.21 % Allowed : 10.18 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.54 (0.30), residues: 768 helix: 1.50 (0.27), residues: 383 sheet: 0.54 (0.69), residues: 59 loop : -1.07 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 165 HIS 0.007 0.002 HIS A 241 PHE 0.017 0.002 PHE A 369 TYR 0.016 0.002 TYR A 158 ARG 0.004 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.756 Fit side-chains REVERT: A 74 LYS cc_start: 0.8227 (tttt) cc_final: 0.7992 (tttt) REVERT: A 75 GLU cc_start: 0.7758 (tt0) cc_final: 0.7458 (tt0) REVERT: A 299 ASP cc_start: 0.8079 (m-30) cc_final: 0.7859 (m-30) REVERT: A 435 GLU cc_start: 0.7598 (mp0) cc_final: 0.7030 (mp0) REVERT: A 474 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7329 (mpp) REVERT: A 491 VAL cc_start: 0.8524 (t) cc_final: 0.8156 (p) REVERT: B 395 VAL cc_start: 0.8309 (p) cc_final: 0.8037 (t) REVERT: B 433 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8240 (t) outliers start: 15 outliers final: 11 residues processed: 156 average time/residue: 0.1766 time to fit residues: 37.0626 Evaluate side-chains 163 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 0.0040 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.0070 chunk 73 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100011 restraints weight = 21821.891| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.82 r_work: 0.3121 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6547 Z= 0.213 Angle : 0.521 5.870 8897 Z= 0.274 Chirality : 0.042 0.252 949 Planarity : 0.004 0.037 1141 Dihedral : 4.907 55.090 988 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.21 % Allowed : 10.77 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.30), residues: 768 helix: 1.59 (0.27), residues: 381 sheet: 0.54 (0.69), residues: 59 loop : -0.93 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.005 0.001 HIS A 401 PHE 0.013 0.001 PHE A 369 TYR 0.014 0.001 TYR B 396 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8062 (tttt) cc_final: 0.7820 (tttt) REVERT: A 75 GLU cc_start: 0.7601 (tt0) cc_final: 0.7276 (tt0) REVERT: A 202 TYR cc_start: 0.8282 (t80) cc_final: 0.7803 (t80) REVERT: A 299 ASP cc_start: 0.7925 (m-30) cc_final: 0.7691 (m-30) REVERT: A 474 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7089 (mpp) REVERT: A 491 VAL cc_start: 0.8369 (t) cc_final: 0.7994 (p) REVERT: A 564 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 395 VAL cc_start: 0.8167 (p) cc_final: 0.7795 (t) REVERT: B 433 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8110 (t) outliers start: 15 outliers final: 10 residues processed: 157 average time/residue: 0.1773 time to fit residues: 37.3309 Evaluate side-chains 153 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100238 restraints weight = 18357.379| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.54 r_work: 0.3141 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6547 Z= 0.225 Angle : 0.522 5.567 8897 Z= 0.275 Chirality : 0.042 0.258 949 Planarity : 0.004 0.037 1141 Dihedral : 4.835 54.867 988 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 10.91 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.30), residues: 768 helix: 1.62 (0.27), residues: 381 sheet: 0.58 (0.69), residues: 59 loop : -0.89 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.015 0.001 TYR A 587 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8053 (tttt) cc_final: 0.7796 (tttt) REVERT: A 75 GLU cc_start: 0.7561 (tt0) cc_final: 0.7264 (tt0) REVERT: A 202 TYR cc_start: 0.8291 (t80) cc_final: 0.7864 (t80) REVERT: A 299 ASP cc_start: 0.7937 (m-30) cc_final: 0.7708 (m-30) REVERT: A 474 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7132 (mpp) REVERT: A 475 LYS cc_start: 0.7680 (ptmm) cc_final: 0.7428 (tttp) REVERT: A 491 VAL cc_start: 0.8349 (t) cc_final: 0.7982 (p) REVERT: A 564 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 433 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8106 (t) outliers start: 16 outliers final: 10 residues processed: 156 average time/residue: 0.1769 time to fit residues: 36.8953 Evaluate side-chains 151 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099315 restraints weight = 20684.460| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.72 r_work: 0.3127 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6547 Z= 0.264 Angle : 0.540 5.978 8897 Z= 0.283 Chirality : 0.043 0.265 949 Planarity : 0.004 0.038 1141 Dihedral : 4.889 55.074 988 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 11.80 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.30), residues: 768 helix: 1.57 (0.27), residues: 384 sheet: 0.58 (0.68), residues: 59 loop : -0.89 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 369 TYR 0.014 0.002 TYR A 587 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8075 (tttt) cc_final: 0.7831 (tttt) REVERT: A 75 GLU cc_start: 0.7568 (tt0) cc_final: 0.7266 (tt0) REVERT: A 202 TYR cc_start: 0.8304 (t80) cc_final: 0.7804 (t80) REVERT: A 299 ASP cc_start: 0.7951 (m-30) cc_final: 0.7731 (m-30) REVERT: A 424 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 474 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7187 (mpp) REVERT: A 475 LYS cc_start: 0.7697 (ptmm) cc_final: 0.7447 (tttp) REVERT: A 491 VAL cc_start: 0.8378 (t) cc_final: 0.8008 (p) REVERT: A 564 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 395 VAL cc_start: 0.8169 (p) cc_final: 0.7831 (t) REVERT: B 433 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8144 (t) outliers start: 16 outliers final: 11 residues processed: 158 average time/residue: 0.1748 time to fit residues: 36.9252 Evaluate side-chains 165 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 0.1980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099825 restraints weight = 20052.887| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.68 r_work: 0.3138 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6547 Z= 0.234 Angle : 0.530 5.967 8897 Z= 0.279 Chirality : 0.043 0.267 949 Planarity : 0.004 0.037 1141 Dihedral : 4.837 54.936 988 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.65 % Allowed : 12.24 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.30), residues: 768 helix: 1.62 (0.27), residues: 381 sheet: 0.60 (0.67), residues: 60 loop : -0.85 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.015 0.001 TYR A 587 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8053 (tttt) cc_final: 0.7816 (tttt) REVERT: A 75 GLU cc_start: 0.7554 (tt0) cc_final: 0.7252 (tt0) REVERT: A 202 TYR cc_start: 0.8293 (t80) cc_final: 0.7803 (t80) REVERT: A 299 ASP cc_start: 0.7932 (m-30) cc_final: 0.7717 (m-30) REVERT: A 424 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 474 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7115 (mpp) REVERT: A 475 LYS cc_start: 0.7679 (ptmm) cc_final: 0.7436 (tttp) REVERT: A 491 VAL cc_start: 0.8354 (t) cc_final: 0.7978 (p) REVERT: B 433 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8112 (t) outliers start: 18 outliers final: 14 residues processed: 147 average time/residue: 0.1790 time to fit residues: 35.3490 Evaluate side-chains 150 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 53 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099786 restraints weight = 25728.600| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.10 r_work: 0.3121 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6547 Z= 0.209 Angle : 0.520 5.949 8897 Z= 0.273 Chirality : 0.042 0.270 949 Planarity : 0.004 0.036 1141 Dihedral : 4.756 54.633 988 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.51 % Allowed : 12.39 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.30), residues: 768 helix: 1.68 (0.27), residues: 380 sheet: 0.48 (0.68), residues: 59 loop : -0.79 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE A 369 TYR 0.015 0.001 TYR A 587 ARG 0.003 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7616 (tt0) cc_final: 0.7302 (tt0) REVERT: A 202 TYR cc_start: 0.8316 (t80) cc_final: 0.7887 (t80) REVERT: A 299 ASP cc_start: 0.7962 (m-30) cc_final: 0.7745 (m-30) REVERT: A 424 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 474 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7161 (mpp) REVERT: A 475 LYS cc_start: 0.7710 (ptmm) cc_final: 0.7476 (tttp) REVERT: A 491 VAL cc_start: 0.8348 (t) cc_final: 0.7973 (p) REVERT: B 433 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8139 (t) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 0.1884 time to fit residues: 36.6925 Evaluate side-chains 154 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098322 restraints weight = 21481.672| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.79 r_work: 0.3102 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6547 Z= 0.334 Angle : 0.577 6.325 8897 Z= 0.303 Chirality : 0.045 0.280 949 Planarity : 0.004 0.039 1141 Dihedral : 4.948 55.247 988 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 12.83 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.30), residues: 768 helix: 1.50 (0.27), residues: 384 sheet: 0.56 (0.67), residues: 60 loop : -0.91 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.007 0.002 HIS A 241 PHE 0.016 0.002 PHE A 369 TYR 0.016 0.002 TYR A 158 ARG 0.004 0.001 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.14 seconds wall clock time: 64 minutes 25.22 seconds (3865.22 seconds total)