Starting phenix.real_space_refine on Mon Jul 28 22:41:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r87_24310/07_2025/7r87_24310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r87_24310/07_2025/7r87_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_24310/07_2025/7r87_24310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r87_24310/07_2025/7r87_24310.map" model { file = "/net/cci-nas-00/data/ceres_data/7r87_24310/07_2025/7r87_24310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r87_24310/07_2025/7r87_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.88, per 1000 atoms: 0.64 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: 2.62 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: 1.15 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: 3.40 Time building geometry restraints manager: 3.12 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: 73.610 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.430 ------------------------------------------------------------------------------- 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 11028 Z= 0.089 Angle : 0.436 6.734 14926 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 Details of bonding type rmsd hydrogen bonds : bond 0.14687 ( 593) hydrogen bonds : angle 5.10812 ( 1731) SS BOND : bond 0.00031 ( 3) SS BOND : angle 0.06584 ( 6) covalent geometry : bond 0.00162 (11025) covalent geometry : angle 0.43652 (14920) *********************** 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 : 1.093 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: 0.2599 time to fit residues: 93.9746 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 : 1.180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109910 restraints weight = 13971.138| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.83 r_work: 0.2982 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 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 11028 Z= 0.210 Angle : 0.641 10.264 14926 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 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 593) hydrogen bonds : angle 3.97079 ( 1731) SS BOND : bond 0.00309 ( 3) SS BOND : angle 0.37886 ( 6) covalent geometry : bond 0.00497 (11025) covalent geometry : angle 0.64128 (14920) *********************** 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 : 0.991 Fit side-chains REVERT: A 165 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7453 (tp40) REVERT: A 299 ASP cc_start: 0.8445 (m-30) cc_final: 0.8192 (m-30) REVERT: A 624 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 33 ASP cc_start: 0.7987 (t0) cc_final: 0.7757 (t0) REVERT: B 213 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8235 (pp) REVERT: B 220 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8316 (mtm-85) REVERT: B 477 MET cc_start: 0.9038 (tmm) cc_final: 0.8724 (ttp) REVERT: B 513 MET cc_start: 0.6549 (ttp) cc_final: 0.6138 (ttp) REVERT: B 517 TRP cc_start: 0.7821 (m100) cc_final: 0.7176 (t60) REVERT: B 613 TYR cc_start: 0.5426 (OUTLIER) cc_final: 0.4783 (p90) REVERT: B 628 LYS cc_start: 0.4371 (tttt) cc_final: 0.4148 (ttpt) REVERT: C 81 TYR cc_start: 0.8612 (m-80) cc_final: 0.8086 (m-80) outliers start: 30 outliers final: 14 residues processed: 193 average time/residue: 0.2711 time to fit residues: 72.4090 Evaluate side-chains 153 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 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 115 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105340 restraints weight = 13984.151| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.78 r_work: 0.2979 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11028 Z= 0.151 Angle : 0.538 9.665 14926 Z= 0.270 Chirality : 0.040 0.174 1698 Planarity : 0.004 0.050 1879 Dihedral : 3.854 56.015 1503 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.29 % Allowed : 12.36 % Favored : 85.35 % 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: 0.38 (0.23), residues: 1349 helix: 1.74 (0.20), residues: 705 sheet: -0.67 (0.36), residues: 183 loop : -1.75 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 593) hydrogen bonds : angle 3.71983 ( 1731) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.25298 ( 6) covalent geometry : bond 0.00362 (11025) covalent geometry : angle 0.53787 (14920) *********************** 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 163 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.022 Fit side-chains REVERT: A 165 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7470 (tp40) REVERT: A 470 HIS cc_start: 0.9427 (OUTLIER) cc_final: 0.9072 (p-80) REVERT: A 624 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8195 (t80) REVERT: B 33 ASP cc_start: 0.8026 (t0) cc_final: 0.7668 (t0) REVERT: B 50 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7462 (ttm110) REVERT: B 213 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8224 (pp) REVERT: B 220 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8257 (mtm-85) REVERT: B 513 MET cc_start: 0.6560 (ttp) cc_final: 0.5909 (mmm) REVERT: B 517 TRP cc_start: 0.7871 (m100) cc_final: 0.7166 (t60) REVERT: B 613 TYR cc_start: 0.5749 (OUTLIER) cc_final: 0.4816 (p90) REVERT: C 81 TYR cc_start: 0.8741 (m-80) cc_final: 0.8207 (m-80) outliers start: 27 outliers final: 16 residues processed: 156 average time/residue: 0.3077 time to fit residues: 67.7543 Evaluate side-chains 146 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 401 LEU 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 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 D residue 94 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099091 restraints weight = 13961.893| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.73 r_work: 0.2885 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11028 Z= 0.221 Angle : 0.606 10.457 14926 Z= 0.303 Chirality : 0.043 0.197 1698 Planarity : 0.004 0.045 1879 Dihedral : 4.182 56.477 1503 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.22 % Allowed : 12.19 % Favored : 84.59 % 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: 0.49 (0.23), residues: 1349 helix: 1.70 (0.19), residues: 708 sheet: -0.56 (0.36), residues: 192 loop : -1.52 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.003 0.001 HIS A 294 PHE 0.022 0.002 PHE B 93 TYR 0.015 0.002 TYR B 507 ARG 0.010 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 593) hydrogen bonds : angle 3.90065 ( 1731) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.37451 ( 6) covalent geometry : bond 0.00540 (11025) covalent geometry : angle 0.60634 (14920) *********************** 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 163 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.167 Fit side-chains REVERT: A 165 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7589 (tp40) REVERT: A 624 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8279 (t80) REVERT: B 50 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7330 (ttm110) REVERT: B 213 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8432 (pp) REVERT: B 220 ARG cc_start: 0.8641 (mtt-85) cc_final: 0.8282 (mtm-85) REVERT: B 517 TRP cc_start: 0.7892 (m100) cc_final: 0.7283 (t60) REVERT: B 558 MET cc_start: 0.8723 (ttm) cc_final: 0.8515 (mtp) REVERT: B 613 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5079 (p90) REVERT: B 628 LYS cc_start: 0.4666 (tttt) cc_final: 0.4140 (mmmt) REVERT: C 32 GLN cc_start: 0.8940 (mp10) cc_final: 0.8710 (mp10) REVERT: C 81 TYR cc_start: 0.8954 (m-80) cc_final: 0.8524 (m-80) REVERT: D 114 TYR cc_start: 0.9184 (t80) cc_final: 0.8976 (t80) outliers start: 38 outliers final: 22 residues processed: 154 average time/residue: 0.2445 time to fit residues: 53.2406 Evaluate side-chains 143 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 353 MET Chi-restraints excluded: chain A residue 401 LEU 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 29 SER 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 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 100 optimal weight: 0.0870 chunk 79 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 overall best weight: 1.2960 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.122356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.100170 restraints weight = 14014.545| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.73 r_work: 0.2901 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11028 Z= 0.160 Angle : 0.558 11.519 14926 Z= 0.277 Chirality : 0.041 0.190 1698 Planarity : 0.004 0.046 1879 Dihedral : 4.100 56.800 1503 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: 0.76 (0.23), residues: 1349 helix: 1.91 (0.19), residues: 705 sheet: -0.32 (0.37), residues: 191 loop : -1.41 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS B 270 PHE 0.020 0.001 PHE B 93 TYR 0.018 0.001 TYR B 507 ARG 0.006 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 593) hydrogen bonds : angle 3.77267 ( 1731) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.35011 ( 6) covalent geometry : bond 0.00382 (11025) covalent geometry : angle 0.55795 (14920) *********************** 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 152 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.135 Fit side-chains REVERT: A 165 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7566 (tp40) REVERT: A 454 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7524 (mm-40) REVERT: A 550 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7984 (tpm170) REVERT: A 624 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8153 (t80) REVERT: B 50 ARG cc_start: 0.7592 (ttm110) cc_final: 0.7039 (ttm110) REVERT: B 213 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8370 (pp) REVERT: B 220 ARG cc_start: 0.8609 (mtt-85) cc_final: 0.8251 (mtm-85) REVERT: B 517 TRP cc_start: 0.7884 (m100) cc_final: 0.7288 (t60) REVERT: B 613 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5150 (p90) REVERT: B 628 LYS cc_start: 0.4702 (tttt) cc_final: 0.4193 (mmmt) REVERT: C 32 GLN cc_start: 0.8934 (mp10) cc_final: 0.8705 (mp10) REVERT: C 54 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7973 (mm-30) REVERT: C 81 TYR cc_start: 0.8933 (m-80) cc_final: 0.8519 (m-80) outliers start: 32 outliers final: 21 residues processed: 141 average time/residue: 0.2368 time to fit residues: 47.4760 Evaluate side-chains 141 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 401 LEU 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 630 PHE Chi-restraints excluded: chain B residue 29 SER 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 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 17 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.118166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.095780 restraints weight = 14221.645| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.76 r_work: 0.2837 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11028 Z= 0.262 Angle : 0.636 11.930 14926 Z= 0.318 Chirality : 0.044 0.197 1698 Planarity : 0.004 0.048 1879 Dihedral : 4.394 56.889 1503 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.88 % Allowed : 13.55 % Favored : 83.57 % 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: 0.64 (0.23), residues: 1349 helix: 1.73 (0.19), residues: 704 sheet: -0.29 (0.37), residues: 191 loop : -1.34 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 584 HIS 0.004 0.001 HIS A 493 PHE 0.020 0.002 PHE B 93 TYR 0.030 0.002 TYR A 628 ARG 0.005 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 593) hydrogen bonds : angle 3.99138 ( 1731) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.48171 ( 6) covalent geometry : bond 0.00642 (11025) covalent geometry : angle 0.63647 (14920) *********************** 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 158 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.136 Fit side-chains REVERT: A 66 ARG cc_start: 0.7123 (mmt180) cc_final: 0.6453 (mmp80) REVERT: A 165 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7605 (tp40) REVERT: A 207 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9050 (tp) REVERT: A 454 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.7534 (mm-40) REVERT: A 624 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 625 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8830 (mt) REVERT: B 213 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8531 (pp) REVERT: B 220 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8317 (mtm-85) REVERT: B 237 ASP cc_start: 0.8716 (m-30) cc_final: 0.8462 (m-30) REVERT: B 267 ILE cc_start: 0.9119 (mt) cc_final: 0.8914 (tt) REVERT: B 503 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8655 (tm-30) REVERT: B 517 TRP cc_start: 0.7950 (m100) cc_final: 0.7367 (t60) REVERT: B 613 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5334 (p90) REVERT: B 628 LYS cc_start: 0.4779 (tttt) cc_final: 0.4288 (mmmt) REVERT: C 32 GLN cc_start: 0.8940 (mp10) cc_final: 0.8709 (mp10) REVERT: C 81 TYR cc_start: 0.9041 (m-80) cc_final: 0.8676 (m-80) outliers start: 34 outliers final: 23 residues processed: 147 average time/residue: 0.2618 time to fit residues: 56.2763 Evaluate side-chains 148 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 401 LEU 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 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 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 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.119889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.097700 restraints weight = 14190.222| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.72 r_work: 0.2864 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11028 Z= 0.192 Angle : 0.585 11.514 14926 Z= 0.291 Chirality : 0.041 0.186 1698 Planarity : 0.004 0.048 1879 Dihedral : 4.275 57.034 1503 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.79 % Allowed : 14.14 % Favored : 83.07 % 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: 0.83 (0.24), residues: 1349 helix: 1.89 (0.19), residues: 703 sheet: -0.09 (0.39), residues: 190 loop : -1.31 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.003 0.001 HIS B 531 PHE 0.019 0.001 PHE B 93 TYR 0.020 0.002 TYR A 628 ARG 0.005 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 593) hydrogen bonds : angle 3.85165 ( 1731) SS BOND : bond 0.00219 ( 3) SS BOND : angle 0.45200 ( 6) covalent geometry : bond 0.00465 (11025) covalent geometry : angle 0.58551 (14920) *********************** 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 153 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.125 Fit side-chains REVERT: A 66 ARG cc_start: 0.7133 (mmt180) cc_final: 0.6668 (mmp80) REVERT: A 165 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7594 (tp40) REVERT: A 207 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9005 (tp) REVERT: A 454 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: A 624 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8146 (t80) REVERT: A 625 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8767 (mt) REVERT: B 50 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7028 (ttm110) REVERT: B 213 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8500 (pp) REVERT: B 220 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.8275 (mtm-85) REVERT: B 237 ASP cc_start: 0.8686 (m-30) cc_final: 0.8426 (m-30) REVERT: B 517 TRP cc_start: 0.7921 (m100) cc_final: 0.7352 (t60) REVERT: B 613 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.5271 (p90) REVERT: B 628 LYS cc_start: 0.4851 (tttt) cc_final: 0.4409 (mmmt) REVERT: C 32 GLN cc_start: 0.8939 (mp10) cc_final: 0.8716 (mp10) REVERT: C 54 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7946 (mt-10) REVERT: C 81 TYR cc_start: 0.9014 (m-80) cc_final: 0.8672 (m-80) outliers start: 33 outliers final: 24 residues processed: 145 average time/residue: 0.2356 time to fit residues: 48.3361 Evaluate side-chains 147 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 401 LEU 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 465 LEU 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 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 116 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** B 271 GLN D 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098052 restraints weight = 14105.449| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.72 r_work: 0.2873 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11028 Z= 0.169 Angle : 0.571 11.378 14926 Z= 0.282 Chirality : 0.041 0.187 1698 Planarity : 0.004 0.048 1879 Dihedral : 4.206 56.657 1503 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.79 % Allowed : 14.99 % Favored : 82.22 % 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: 0.96 (0.24), residues: 1349 helix: 2.00 (0.19), residues: 702 sheet: -0.05 (0.39), residues: 190 loop : -1.26 (0.30), residues: 457 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 0.018 0.001 PHE B 93 TYR 0.017 0.001 TYR B 507 ARG 0.003 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 593) hydrogen bonds : angle 3.80736 ( 1731) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.43564 ( 6) covalent geometry : bond 0.00408 (11025) covalent geometry : angle 0.57131 (14920) *********************** 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 154 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.526 Fit side-chains REVERT: A 66 ARG cc_start: 0.7129 (mmt180) cc_final: 0.6679 (mmp80) REVERT: A 165 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7632 (tp40) REVERT: A 207 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8982 (tp) REVERT: A 454 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7399 (mm-40) REVERT: A 624 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 625 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8762 (mt) REVERT: B 213 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8513 (pp) REVERT: B 220 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.8252 (mtm-85) REVERT: B 343 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7641 (mm-40) REVERT: B 517 TRP cc_start: 0.7928 (m100) cc_final: 0.7353 (t60) REVERT: B 613 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5275 (p90) REVERT: B 628 LYS cc_start: 0.4836 (tttt) cc_final: 0.4407 (mmmt) REVERT: C 32 GLN cc_start: 0.8947 (mp10) cc_final: 0.8726 (mp10) REVERT: C 54 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7970 (mt-10) REVERT: C 81 TYR cc_start: 0.9007 (m-80) cc_final: 0.8684 (m-80) outliers start: 33 outliers final: 24 residues processed: 145 average time/residue: 0.2571 time to fit residues: 52.7566 Evaluate side-chains 144 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 401 LEU 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 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 271 GLN 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 465 LEU 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 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 23 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 92 optimal weight: 0.0030 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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** B 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.101945 restraints weight = 14298.254| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.80 r_work: 0.2891 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11028 Z= 0.115 Angle : 0.538 11.011 14926 Z= 0.263 Chirality : 0.039 0.202 1698 Planarity : 0.003 0.049 1879 Dihedral : 4.031 55.817 1503 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.46 % Allowed : 15.24 % Favored : 82.30 % 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: 1.16 (0.24), residues: 1349 helix: 2.18 (0.20), residues: 702 sheet: 0.04 (0.39), residues: 190 loop : -1.19 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.016 0.001 PHE B 93 TYR 0.018 0.001 TYR B 507 ARG 0.004 0.000 ARG B 610 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 593) hydrogen bonds : angle 3.65316 ( 1731) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.37718 ( 6) covalent geometry : bond 0.00264 (11025) covalent geometry : angle 0.53850 (14920) *********************** 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 156 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.199 Fit side-chains REVERT: A 66 ARG cc_start: 0.7015 (mmt180) cc_final: 0.6559 (mmp80) REVERT: A 165 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7567 (tp40) REVERT: A 344 ARG cc_start: 0.8812 (tmm-80) cc_final: 0.8388 (tmm-80) REVERT: A 454 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7244 (mm-40) REVERT: A 470 HIS cc_start: 0.9399 (OUTLIER) cc_final: 0.9028 (p-80) REVERT: A 550 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7928 (tpm170) REVERT: A 624 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8035 (t80) REVERT: B 213 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8433 (pp) REVERT: B 220 ARG cc_start: 0.8609 (mtt-85) cc_final: 0.8188 (mtm-85) REVERT: B 237 ASP cc_start: 0.8530 (m-30) cc_final: 0.8259 (m-30) REVERT: B 343 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7597 (mm-40) REVERT: B 517 TRP cc_start: 0.7890 (m100) cc_final: 0.7312 (t60) REVERT: B 613 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.5125 (p90) REVERT: B 615 MET cc_start: 0.8044 (tpt) cc_final: 0.7653 (tpt) REVERT: B 628 LYS cc_start: 0.4913 (tttt) cc_final: 0.4420 (mmmt) REVERT: C 54 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8019 (mt-10) REVERT: C 81 TYR cc_start: 0.8931 (m-80) cc_final: 0.8546 (m-80) REVERT: D 37 GLU cc_start: 0.8644 (pt0) cc_final: 0.8338 (pm20) outliers start: 29 outliers final: 17 residues processed: 149 average time/residue: 0.3484 time to fit residues: 73.6234 Evaluate side-chains 142 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 401 LEU 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 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 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 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 131 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.096616 restraints weight = 14303.822| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.78 r_work: 0.2827 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11028 Z= 0.260 Angle : 0.653 11.981 14926 Z= 0.321 Chirality : 0.044 0.203 1698 Planarity : 0.004 0.050 1879 Dihedral : 4.401 57.078 1503 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.46 % Allowed : 15.41 % Favored : 82.13 % 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: 0.86 (0.24), residues: 1349 helix: 1.87 (0.19), residues: 704 sheet: -0.15 (0.39), residues: 196 loop : -1.21 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 584 HIS 0.005 0.001 HIS A 493 PHE 0.019 0.002 PHE B 93 TYR 0.024 0.002 TYR A 628 ARG 0.004 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 593) hydrogen bonds : angle 3.92494 ( 1731) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.56092 ( 6) covalent geometry : bond 0.00637 (11025) covalent geometry : angle 0.65340 (14920) ********************** 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 148 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.319 Fit side-chains REVERT: A 66 ARG cc_start: 0.7067 (mmt180) cc_final: 0.6635 (mmp80) REVERT: A 165 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7578 (tp40) REVERT: A 454 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: A 624 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8135 (t80) REVERT: B 213 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8542 (pp) REVERT: B 220 ARG cc_start: 0.8666 (mtt-85) cc_final: 0.8291 (mtm-85) REVERT: B 237 ASP cc_start: 0.8649 (m-30) cc_final: 0.8383 (m-30) REVERT: B 343 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7611 (mm-40) REVERT: B 517 TRP cc_start: 0.7970 (m100) cc_final: 0.7364 (t60) REVERT: B 613 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5042 (p90) REVERT: B 628 LYS cc_start: 0.4847 (tttt) cc_final: 0.4317 (mmmt) REVERT: C 32 GLN cc_start: 0.8948 (mp10) cc_final: 0.8727 (mp10) REVERT: C 81 TYR cc_start: 0.9026 (m-80) cc_final: 0.8737 (m-80) outliers start: 29 outliers final: 25 residues processed: 139 average time/residue: 0.2975 time to fit residues: 57.4478 Evaluate side-chains 144 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 401 LEU 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 322 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 465 LEU 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 D residue 25 THR 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 122 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN B 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.097006 restraints weight = 14252.966| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.77 r_work: 0.2807 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 11028 Z= 0.238 Angle : 0.905 59.167 14926 Z= 0.503 Chirality : 0.049 1.031 1698 Planarity : 0.004 0.051 1879 Dihedral : 4.402 57.153 1503 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.46 % Allowed : 15.33 % Favored : 82.22 % Cbeta Deviations : 0.08 % 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: 0.86 (0.24), residues: 1349 helix: 1.89 (0.19), residues: 704 sheet: -0.16 (0.39), residues: 196 loop : -1.23 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 584 HIS 0.004 0.001 HIS A 493 PHE 0.019 0.002 PHE B 93 TYR 0.022 0.002 TYR A 628 ARG 0.007 0.000 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 593) hydrogen bonds : angle 3.92322 ( 1731) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.50154 ( 6) covalent geometry : bond 0.00557 (11025) covalent geometry : angle 0.90559 (14920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5677.14 seconds wall clock time: 103 minutes 47.26 seconds (6227.26 seconds total)