Starting phenix.real_space_refine on Sun Dec 29 15:03:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r87_24310/12_2024/7r87_24310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r87_24310/12_2024/7r87_24310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r87_24310/12_2024/7r87_24310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r87_24310/12_2024/7r87_24310.map" model { file = "/net/cci-nas-00/data/ceres_data/7r87_24310/12_2024/7r87_24310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r87_24310/12_2024/7r87_24310.cif" } resolution = 3.4 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= 0.002 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 67 5.16 5 C 6966 2.51 5 N 1827 2.21 5 O 1933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10793 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4608 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 21, 'TRANS': 564} Chain breaks: 2 Chain: "B" Number of atoms: 4481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4481 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 539} Chain breaks: 4 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Time building chain proxies: 6.50, per 1000 atoms: 0.60 Number of scatterers: 10793 At special positions: 0 Unit cell: (113.288, 104.958, 126.616, 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 67 16.00 O 1933 8.00 N 1827 7.00 C 6966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " 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 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.5 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 53.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.390A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.504A pdb=" N VAL A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 331 removed outlier: 3.583A pdb=" N GLU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.916A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.571A pdb=" N VAL A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.134A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.567A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.562A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.277A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 4.157A pdb=" N PHE A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 617 removed outlier: 4.239A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 619 through 649 removed outlier: 4.577A pdb=" N ILE A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 4.572A pdb=" N HIS A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 removed outlier: 3.556A pdb=" N VAL B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 244 through 261 removed outlier: 3.518A pdb=" N GLY B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.639A pdb=" N LEU B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.925A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.615A pdb=" N GLU B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 458 through 473 removed outlier: 4.333A pdb=" N ASN B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 removed outlier: 3.516A pdb=" N GLY B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 513 removed outlier: 4.628A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.685A pdb=" N TRP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 3.511A pdb=" N TRP B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.592A pdb=" N SER B 637 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR B 638 " --> pdb=" O LEU B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.640A pdb=" N ASP D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.936A pdb=" N LYS A 70 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR A 45 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.936A pdb=" N LYS A 70 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR A 45 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA A 43 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 110 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.522A pdb=" N THR A 248 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 81 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA A 264 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS A 83 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU A 266 " --> pdb=" O CYS A 83 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 85 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 96 removed outlier: 7.445A pdb=" N PHE B 93 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG B 50 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 95 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU B 48 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.620A pdb=" N SER B 268 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 105 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET B 100 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU B 284 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 102 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET B 286 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 104 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.537A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.736A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 107 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1731 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: 3.80 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3438 1.34 - 1.46: 2397 1.46 - 1.58: 5083 1.58 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 11025 Sorted by residual: bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.05e+00 bond pdb=" CB PRO B 514 " pdb=" CG PRO B 514 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.47e-01 bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.51e-02 4.39e+03 7.01e-01 bond pdb=" CA ILE B 459 " pdb=" C ILE B 459 " ideal model delta sigma weight residual 1.524 1.533 -0.008 1.05e-02 9.07e+03 6.53e-01 bond pdb=" CA PRO B 514 " pdb=" CB PRO B 514 " ideal model delta sigma weight residual 1.531 1.536 -0.005 6.20e-03 2.60e+04 5.94e-01 ... (remaining 11020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 14625 1.35 - 2.69: 232 2.69 - 4.04: 42 4.04 - 5.39: 14 5.39 - 6.73: 7 Bond angle restraints: 14920 Sorted by residual: angle pdb=" N ILE A 416 " pdb=" CA ILE A 416 " pdb=" C ILE A 416 " ideal model delta sigma weight residual 112.96 109.27 3.69 1.00e+00 1.00e+00 1.36e+01 angle pdb=" N ILE B 307 " pdb=" CA ILE B 307 " pdb=" C ILE B 307 " ideal model delta sigma weight residual 113.07 108.80 4.27 1.36e+00 5.41e-01 9.88e+00 angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 122.08 126.15 -4.07 1.47e+00 4.63e-01 7.66e+00 angle pdb=" C MET B 513 " pdb=" N PRO B 514 " pdb=" CA PRO B 514 " ideal model delta sigma weight residual 121.65 119.14 2.51 1.01e+00 9.80e-01 6.16e+00 angle pdb=" C ASN A 551 " pdb=" N ILE A 552 " pdb=" CA ILE A 552 " ideal model delta sigma weight residual 120.62 124.60 -3.98 1.64e+00 3.72e-01 5.90e+00 ... (remaining 14915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6085 17.58 - 35.16: 394 35.16 - 52.73: 66 52.73 - 70.31: 13 70.31 - 87.89: 7 Dihedral angle restraints: 6565 sinusoidal: 2612 harmonic: 3953 Sorted by residual: dihedral pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " pdb=" OE1 GLU A 452 " ideal model delta sinusoidal sigma weight residual 0.00 -85.10 85.10 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CA ARG A 157 " pdb=" CB ARG A 157 " pdb=" CG ARG A 157 " pdb=" CD ARG A 157 " ideal model delta sinusoidal sigma weight residual -180.00 -121.93 -58.07 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLN A 126 " pdb=" CB GLN A 126 " pdb=" CG GLN A 126 " pdb=" CD GLN A 126 " ideal model delta sinusoidal sigma weight residual 60.00 113.64 -53.64 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 6562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1143 0.027 - 0.054: 342 0.054 - 0.082: 118 0.082 - 0.109: 73 0.109 - 0.136: 22 Chirality restraints: 1698 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA THR A 430 " pdb=" N THR A 430 " pdb=" C THR A 430 " pdb=" CB THR A 430 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE C 90 " pdb=" N ILE C 90 " pdb=" C ILE C 90 " pdb=" CB ILE C 90 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1695 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 555 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO A 556 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 556 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 556 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO B 491 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.016 5.00e-02 4.00e+02 2.50e-02 9.97e-01 pdb=" N PRO A 277 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.014 5.00e-02 4.00e+02 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3492 2.83 - 3.35: 9734 3.35 - 3.87: 17750 3.87 - 4.38: 19445 4.38 - 4.90: 35334 Nonbonded interactions: 85755 Sorted by model distance: nonbonded pdb=" O SER B 288 " pdb=" OG SER B 288 " model vdw 2.317 3.040 nonbonded pdb=" O LYS B 605 " pdb=" OG SER B 609 " model vdw 2.327 3.040 nonbonded pdb=" O ARG A 550 " pdb=" NH1 ARG A 550 " model vdw 2.343 3.120 nonbonded pdb=" OE1 GLN A 417 " pdb=" ND2 ASN B 579 " model vdw 2.349 3.120 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.355 3.040 ... (remaining 85750 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: 1.330 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: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.550 Find NCS groups from input model: 0.170 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.002 0.043 11025 Z= 0.104 Angle : 0.437 6.734 14920 Z= 0.252 Chirality : 0.036 0.136 1698 Planarity : 0.002 0.025 1879 Dihedral : 12.082 87.888 4020 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.51 % Allowed : 5.33 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -1.48 (0.21), residues: 1349 helix: 0.27 (0.18), residues: 701 sheet: -1.06 (0.36), residues: 181 loop : -2.90 (0.24), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 584 HIS 0.002 0.000 HIS A 470 PHE 0.006 0.000 PHE A 630 TYR 0.006 0.000 TYR B 472 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 1.328 Fit side-chains REVERT: A 241 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7244 (ttp-110) REVERT: A 304 LEU cc_start: 0.8718 (tp) cc_final: 0.8440 (tp) REVERT: B 160 ASN cc_start: 0.6780 (m-40) cc_final: 0.6426 (m-40) REVERT: B 186 LYS cc_start: 0.7744 (tttp) cc_final: 0.7530 (tptm) REVERT: B 220 ARG cc_start: 0.7348 (mtt-85) cc_final: 0.7084 (mtm-85) REVERT: B 481 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7230 (mt-10) REVERT: B 568 ASN cc_start: 0.8192 (m110) cc_final: 0.7986 (m-40) REVERT: B 663 ARG cc_start: 0.7772 (ttt-90) cc_final: 0.7502 (ttt180) outliers start: 6 outliers final: 4 residues processed: 266 average time/residue: 0.2748 time to fit residues: 99.7659 Evaluate side-chains 187 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 116 ASN A 134 GLN A 165 GLN A 206 GLN A 392 GLN A 437 ASN A 462 GLN A 470 HIS A 510 HIS A 528 ASN A 578 ASN A 604 GLN A 607 GLN B 99 GLN B 153 GLN B 183 GLN B 271 GLN B 299 HIS B 302 GLN B 438 HIS B 462 ASN B 526 GLN B 607 GLN C 75 ASN D 26 GLN D 47 GLN D 58 GLN D 65 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11025 Z= 0.321 Angle : 0.641 10.264 14920 Z= 0.323 Chirality : 0.043 0.248 1698 Planarity : 0.005 0.062 1879 Dihedral : 4.086 54.888 1504 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.54 % Allowed : 9.48 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -0.37 (0.22), residues: 1349 helix: 1.08 (0.19), residues: 718 sheet: -1.02 (0.34), residues: 185 loop : -2.09 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.007 0.001 HIS A 510 PHE 0.025 0.002 PHE B 93 TYR 0.019 0.002 TYR B 507 ARG 0.011 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.248 Fit side-chains REVERT: A 41 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8486 (tp) REVERT: A 165 GLN cc_start: 0.7571 (tp-100) cc_final: 0.7118 (tp40) REVERT: A 299 ASP cc_start: 0.7409 (m-30) cc_final: 0.7110 (m-30) REVERT: A 480 MET cc_start: 0.8384 (tpp) cc_final: 0.8142 (mmm) REVERT: A 583 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7236 (pt) REVERT: A 624 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 33 ASP cc_start: 0.7922 (t0) cc_final: 0.7613 (t0) REVERT: B 213 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7168 (pp) REVERT: B 220 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7482 (mtm-85) REVERT: B 513 MET cc_start: 0.5588 (ttp) cc_final: 0.5158 (ttp) REVERT: B 517 TRP cc_start: 0.7476 (m100) cc_final: 0.6411 (t60) REVERT: B 613 TYR cc_start: 0.5155 (OUTLIER) cc_final: 0.4546 (p90) REVERT: B 628 LYS cc_start: 0.3709 (tttt) cc_final: 0.3500 (ttpt) REVERT: B 664 PHE cc_start: 0.8639 (m-10) cc_final: 0.8430 (m-80) REVERT: C 81 TYR cc_start: 0.8317 (m-80) cc_final: 0.7669 (m-80) outliers start: 30 outliers final: 14 residues processed: 193 average time/residue: 0.2689 time to fit residues: 72.3050 Evaluate side-chains 155 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain D residue 94 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN B 271 GLN B 462 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11025 Z= 0.178 Angle : 0.513 9.295 14920 Z= 0.257 Chirality : 0.039 0.173 1698 Planarity : 0.003 0.048 1879 Dihedral : 3.760 55.893 1503 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.12 % Allowed : 11.69 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.42 (0.23), residues: 1349 helix: 1.77 (0.20), residues: 709 sheet: -0.69 (0.36), residues: 185 loop : -1.75 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS A 510 PHE 0.021 0.001 PHE B 93 TYR 0.017 0.001 TYR B 507 ARG 0.009 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.303 Fit side-chains REVERT: A 165 GLN cc_start: 0.7505 (tp-100) cc_final: 0.7124 (tp40) REVERT: A 470 HIS cc_start: 0.9322 (OUTLIER) cc_final: 0.8784 (p-80) REVERT: A 624 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7763 (t80) REVERT: B 33 ASP cc_start: 0.7956 (t0) cc_final: 0.7640 (t0) REVERT: B 50 ARG cc_start: 0.6908 (ttm110) cc_final: 0.6660 (ttm110) REVERT: B 213 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7146 (pp) REVERT: B 220 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7330 (mtm-85) REVERT: B 513 MET cc_start: 0.5534 (ttp) cc_final: 0.5072 (ttp) REVERT: B 517 TRP cc_start: 0.7428 (m100) cc_final: 0.6257 (t60) REVERT: B 613 TYR cc_start: 0.5298 (OUTLIER) cc_final: 0.4456 (p90) REVERT: B 664 PHE cc_start: 0.8551 (m-10) cc_final: 0.8318 (m-80) REVERT: C 81 TYR cc_start: 0.8350 (m-80) cc_final: 0.7593 (m-80) outliers start: 25 outliers final: 13 residues processed: 158 average time/residue: 0.2490 time to fit residues: 55.4190 Evaluate side-chains 146 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain D residue 94 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 0.0000 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11025 Z= 0.392 Angle : 0.627 10.762 14920 Z= 0.315 Chirality : 0.044 0.205 1698 Planarity : 0.004 0.046 1879 Dihedral : 4.199 56.648 1502 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.13 % Allowed : 12.36 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.48 (0.23), residues: 1349 helix: 1.70 (0.19), residues: 707 sheet: -0.59 (0.36), residues: 192 loop : -1.53 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.003 0.001 HIS B 438 PHE 0.022 0.002 PHE B 93 TYR 0.016 0.002 TYR B 507 ARG 0.009 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.255 Fit side-chains REVERT: A 165 GLN cc_start: 0.7673 (tp-100) cc_final: 0.7295 (tp40) REVERT: A 624 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7840 (t80) REVERT: B 50 ARG cc_start: 0.6794 (ttm110) cc_final: 0.6475 (ttm110) REVERT: B 213 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7434 (pp) REVERT: B 220 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7392 (mtm-85) REVERT: B 517 TRP cc_start: 0.7472 (m100) cc_final: 0.6426 (t60) REVERT: B 613 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4842 (p90) REVERT: B 628 LYS cc_start: 0.3968 (tttt) cc_final: 0.3645 (mmmt) REVERT: C 32 GLN cc_start: 0.8875 (mp10) cc_final: 0.8625 (mp10) REVERT: C 81 TYR cc_start: 0.8599 (m-80) cc_final: 0.8017 (m-80) REVERT: D 37 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8182 (pm20) outliers start: 37 outliers final: 21 residues processed: 148 average time/residue: 0.2460 time to fit residues: 51.7086 Evaluate side-chains 138 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11025 Z= 0.296 Angle : 0.576 11.735 14920 Z= 0.287 Chirality : 0.041 0.189 1698 Planarity : 0.004 0.046 1879 Dihedral : 4.135 56.714 1502 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.71 % Allowed : 13.46 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.68 (0.23), residues: 1349 helix: 1.87 (0.19), residues: 701 sheet: -0.44 (0.37), residues: 191 loop : -1.42 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.006 0.001 HIS B 270 PHE 0.020 0.002 PHE B 93 TYR 0.017 0.001 TYR B 507 ARG 0.005 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.246 Fit side-chains REVERT: A 66 ARG cc_start: 0.6624 (mmt180) cc_final: 0.6039 (mmp80) REVERT: A 165 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7281 (tp40) REVERT: A 454 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7188 (mm-40) REVERT: A 624 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7807 (t80) REVERT: A 628 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: B 50 ARG cc_start: 0.6801 (ttm110) cc_final: 0.6082 (ttm110) REVERT: B 213 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7460 (pp) REVERT: B 220 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.7354 (mtm-85) REVERT: B 517 TRP cc_start: 0.7451 (m100) cc_final: 0.6451 (t60) REVERT: B 613 TYR cc_start: 0.6126 (OUTLIER) cc_final: 0.5065 (p90) REVERT: C 32 GLN cc_start: 0.8878 (mp10) cc_final: 0.8635 (mp10) REVERT: C 81 TYR cc_start: 0.8598 (m-80) cc_final: 0.8090 (m-80) REVERT: D 37 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8182 (pm20) outliers start: 32 outliers final: 21 residues processed: 141 average time/residue: 0.2449 time to fit residues: 48.8263 Evaluate side-chains 141 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN D 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11025 Z= 0.316 Angle : 0.589 11.421 14920 Z= 0.293 Chirality : 0.042 0.202 1698 Planarity : 0.004 0.047 1879 Dihedral : 4.193 56.774 1502 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.79 % Allowed : 13.80 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.76 (0.23), residues: 1349 helix: 1.89 (0.19), residues: 700 sheet: -0.30 (0.38), residues: 190 loop : -1.35 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.003 0.001 HIS A 493 PHE 0.019 0.002 PHE B 93 TYR 0.017 0.002 TYR B 507 ARG 0.005 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.378 Fit side-chains REVERT: A 66 ARG cc_start: 0.6672 (mmt180) cc_final: 0.5928 (mmp80) REVERT: A 165 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7274 (tp40) REVERT: A 454 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: A 624 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7793 (t80) REVERT: A 625 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7938 (mt) REVERT: B 213 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7509 (pp) REVERT: B 220 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7344 (mtm-85) REVERT: B 503 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 517 TRP cc_start: 0.7446 (m100) cc_final: 0.6461 (t60) REVERT: B 558 MET cc_start: 0.7733 (ttm) cc_final: 0.7486 (mtp) REVERT: B 613 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5072 (p90) REVERT: C 32 GLN cc_start: 0.8883 (mp10) cc_final: 0.8642 (mp10) REVERT: C 54 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7659 (mt-10) REVERT: C 81 TYR cc_start: 0.8639 (m-80) cc_final: 0.8165 (m-80) REVERT: D 37 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8105 (pm20) outliers start: 33 outliers final: 22 residues processed: 145 average time/residue: 0.2507 time to fit residues: 51.3586 Evaluate side-chains 143 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 81 optimal weight: 0.0010 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11025 Z= 0.142 Angle : 0.521 10.760 14920 Z= 0.255 Chirality : 0.039 0.193 1698 Planarity : 0.003 0.047 1879 Dihedral : 3.918 55.735 1502 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.62 % Allowed : 14.14 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.10 (0.24), residues: 1349 helix: 2.19 (0.20), residues: 701 sheet: -0.10 (0.39), residues: 190 loop : -1.26 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.003 0.001 HIS B 531 PHE 0.016 0.001 PHE B 93 TYR 0.017 0.001 TYR B 507 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.259 Fit side-chains REVERT: A 165 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7302 (tp40) REVERT: A 454 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.6963 (mm-40) REVERT: A 470 HIS cc_start: 0.9352 (OUTLIER) cc_final: 0.8854 (p-80) REVERT: A 550 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7458 (tpm170) REVERT: A 624 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 50 ARG cc_start: 0.6798 (ttm110) cc_final: 0.6173 (ttm110) REVERT: B 213 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7416 (pp) REVERT: B 220 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.7284 (mtm-85) REVERT: B 343 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7556 (mm-40) REVERT: B 517 TRP cc_start: 0.7440 (m100) cc_final: 0.6454 (t60) REVERT: B 558 MET cc_start: 0.7721 (ttm) cc_final: 0.7483 (mtp) REVERT: B 613 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.5029 (p90) REVERT: B 615 MET cc_start: 0.6934 (tpt) cc_final: 0.6678 (tpt) REVERT: C 32 GLN cc_start: 0.8880 (mp10) cc_final: 0.8641 (mp10) REVERT: C 54 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7750 (mt-10) REVERT: C 81 TYR cc_start: 0.8573 (m-80) cc_final: 0.8036 (m-80) REVERT: D 37 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8095 (pm20) outliers start: 31 outliers final: 17 residues processed: 146 average time/residue: 0.2519 time to fit residues: 52.2646 Evaluate side-chains 138 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11025 Z= 0.252 Angle : 0.572 11.824 14920 Z= 0.278 Chirality : 0.041 0.204 1698 Planarity : 0.003 0.047 1879 Dihedral : 4.033 56.525 1502 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.62 % Allowed : 14.14 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.11 (0.24), residues: 1349 helix: 2.14 (0.19), residues: 703 sheet: -0.01 (0.39), residues: 190 loop : -1.22 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.003 0.001 HIS B 531 PHE 0.017 0.001 PHE B 93 TYR 0.017 0.001 TYR B 507 ARG 0.004 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 1.311 Fit side-chains REVERT: A 165 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7310 (tp40) REVERT: A 454 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.6988 (mm-40) REVERT: A 624 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7750 (t80) REVERT: B 213 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7434 (pp) REVERT: B 220 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7316 (mtm-85) REVERT: B 343 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7543 (mm-40) REVERT: B 517 TRP cc_start: 0.7453 (m100) cc_final: 0.6456 (t60) REVERT: B 613 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5128 (p90) REVERT: B 615 MET cc_start: 0.7064 (tpt) cc_final: 0.6799 (tpt) REVERT: C 54 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7691 (mt-10) REVERT: C 81 TYR cc_start: 0.8611 (m-80) cc_final: 0.8111 (m-80) REVERT: D 37 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8051 (pm20) outliers start: 31 outliers final: 21 residues processed: 142 average time/residue: 0.2436 time to fit residues: 49.2737 Evaluate side-chains 143 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11025 Z= 0.242 Angle : 0.569 12.619 14920 Z= 0.276 Chirality : 0.040 0.205 1698 Planarity : 0.003 0.048 1879 Dihedral : 4.055 56.626 1502 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.37 % Allowed : 14.90 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.12 (0.24), residues: 1349 helix: 2.14 (0.19), residues: 703 sheet: 0.03 (0.39), residues: 190 loop : -1.21 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.003 0.001 HIS B 531 PHE 0.017 0.001 PHE B 93 TYR 0.018 0.001 TYR B 507 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.228 Fit side-chains REVERT: A 66 ARG cc_start: 0.6702 (mmt180) cc_final: 0.6178 (mmp80) REVERT: A 165 GLN cc_start: 0.7635 (tp-100) cc_final: 0.7319 (tp40) REVERT: A 454 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.6967 (mm-40) REVERT: A 624 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7727 (t80) REVERT: B 213 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7438 (pp) REVERT: B 220 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7315 (mtm-85) REVERT: B 343 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7501 (mm-40) REVERT: B 517 TRP cc_start: 0.7444 (m100) cc_final: 0.6444 (t60) REVERT: B 613 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5156 (p90) REVERT: B 615 MET cc_start: 0.7146 (tpt) cc_final: 0.6887 (tpt) REVERT: C 54 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7743 (mt-10) REVERT: C 81 TYR cc_start: 0.8619 (m-80) cc_final: 0.8105 (m-80) REVERT: D 37 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8045 (pm20) outliers start: 28 outliers final: 22 residues processed: 141 average time/residue: 0.2454 time to fit residues: 49.1952 Evaluate side-chains 146 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11025 Z= 0.441 Angle : 0.664 12.785 14920 Z= 0.327 Chirality : 0.044 0.205 1698 Planarity : 0.004 0.049 1879 Dihedral : 4.408 57.382 1502 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.62 % Allowed : 14.39 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.81 (0.23), residues: 1349 helix: 1.84 (0.19), residues: 703 sheet: -0.21 (0.38), residues: 197 loop : -1.22 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 584 HIS 0.005 0.001 HIS B 438 PHE 0.019 0.002 PHE B 93 TYR 0.017 0.002 TYR A 581 ARG 0.004 0.001 ARG B 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.297 Fit side-chains REVERT: A 66 ARG cc_start: 0.6785 (mmt180) cc_final: 0.6298 (mmp80) REVERT: A 165 GLN cc_start: 0.7666 (tp-100) cc_final: 0.7307 (tp40) REVERT: A 454 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7115 (mm-40) REVERT: A 624 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7764 (t80) REVERT: B 213 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7689 (pp) REVERT: B 220 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7402 (mtm-85) REVERT: B 343 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7514 (mm-40) REVERT: B 503 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 517 TRP cc_start: 0.7463 (m100) cc_final: 0.6467 (t60) REVERT: B 613 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.5270 (p90) REVERT: C 32 GLN cc_start: 0.8900 (mp10) cc_final: 0.8666 (mp10) REVERT: C 81 TYR cc_start: 0.8677 (m-80) cc_final: 0.8307 (m-80) REVERT: D 37 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7960 (pm20) outliers start: 31 outliers final: 23 residues processed: 142 average time/residue: 0.2661 time to fit residues: 52.9144 Evaluate side-chains 146 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.123531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101405 restraints weight = 14030.447| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.68 r_work: 0.2903 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11025 Z= 0.179 Angle : 0.558 12.508 14920 Z= 0.269 Chirality : 0.040 0.194 1698 Planarity : 0.003 0.048 1879 Dihedral : 4.068 55.697 1502 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.20 % Allowed : 14.90 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.13 (0.24), residues: 1349 helix: 2.14 (0.20), residues: 703 sheet: -0.02 (0.39), residues: 190 loop : -1.15 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.004 0.001 HIS B 531 PHE 0.017 0.001 PHE B 93 TYR 0.018 0.001 TYR B 507 ARG 0.005 0.000 ARG B 610 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.49 seconds wall clock time: 42 minutes 9.44 seconds (2529.44 seconds total)