Starting phenix.real_space_refine on Thu Jun 4 05:18:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rd9_53930/06_2026/9rd9_53930.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rd9_53930/06_2026/9rd9_53930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rd9_53930/06_2026/9rd9_53930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rd9_53930/06_2026/9rd9_53930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rd9_53930/06_2026/9rd9_53930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rd9_53930/06_2026/9rd9_53930.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4 5.49 5 S 31 5.16 5 C 6688 2.51 5 N 1811 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10537 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6218 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 35, 'TRANS': 757} Chain breaks: 3 Chain: "B" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3978 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 508} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 65 Unusual residues: {' ZN': 1, '6OU': 1, 'CO2': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2530 SG CYS A 351 43.570 58.237 36.144 1.00 43.23 S ATOM 3971 SG CYS A 539 46.072 58.135 39.482 1.00 30.65 S Time building chain proxies: 2.77, per 1000 atoms: 0.26 Number of scatterers: 10537 At special positions: 0 Unit cell: (83.95, 95.63, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 4 15.00 O 2002 8.00 N 1811 7.00 C 6688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 515.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 524 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 539 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 351 " 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 5 sheets defined 67.9% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.748A pdb=" N PHE A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.855A pdb=" N ILE A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 69 through 79 removed outlier: 3.675A pdb=" N PHE A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.562A pdb=" N LEU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.786A pdb=" N GLY A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 227 through 244 removed outlier: 3.591A pdb=" N HIS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.631A pdb=" N GLU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 301 through 329 removed outlier: 3.690A pdb=" N SER A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 367 removed outlier: 3.753A pdb=" N GLU A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.532A pdb=" N ALA A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.623A pdb=" N ARG A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 596 through 601 removed outlier: 4.101A pdb=" N GLY A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 668 through 673 removed outlier: 4.160A pdb=" N THR A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 694 through 721 Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 through 759' Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'B' and resid 7 through 23 removed outlier: 3.517A pdb=" N MET B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Proline residue: B 17 - end of helix Processing helix chain 'B' and resid 31 through 62 Processing helix chain 'B' and resid 76 through 82 Processing helix chain 'B' and resid 89 through 114 removed outlier: 4.066A pdb=" N GLN B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 140 Processing helix chain 'B' and resid 142 through 162 Processing helix chain 'B' and resid 167 through 200 removed outlier: 3.753A pdb=" N PHE B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 218 through 236 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.701A pdb=" N ILE B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.713A pdb=" N VAL B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 281 through 304 removed outlier: 4.208A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 330 Processing helix chain 'B' and resid 332 through 353 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 373 through 395 Processing helix chain 'B' and resid 404 through 427 removed outlier: 4.091A pdb=" N GLN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 457 removed outlier: 3.502A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 491 removed outlier: 3.633A pdb=" N ASP B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.248A pdb=" N THR B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 removed outlier: 3.508A pdb=" N ASN B 511 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 527 removed outlier: 3.847A pdb=" N TRP B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 375 removed outlier: 4.352A pdb=" N CYS A 351 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N HIS A 524 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 519 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA A 583 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 521 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 585 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 523 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 582 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.287A pdb=" N ASP A 384 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLU A 409 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N CYS A 386 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 681 through 684 removed outlier: 6.718A pdb=" N ALA A 663 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N HIS A 684 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE A 665 " --> pdb=" O HIS A 684 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 664 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE A 804 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA5, first strand: chain 'A' and resid 733 through 736 638 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1891 1.33 - 1.45: 2640 1.45 - 1.57: 6016 1.57 - 1.69: 8 1.69 - 1.81: 55 Bond restraints: 10610 Sorted by residual: bond pdb=" C CO2 A 907 " pdb=" O2 CO2 A 907 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C CO2 A 906 " pdb=" O1 CO2 A 906 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C CO2 A 906 " pdb=" O2 CO2 A 906 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C CO2 A 904 " pdb=" O1 CO2 A 904 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C CO2 A 904 " pdb=" O2 CO2 A 904 " ideal model delta sigma weight residual 1.155 1.219 -0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 10605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 14007 1.38 - 2.75: 280 2.75 - 4.13: 72 4.13 - 5.50: 15 5.50 - 6.88: 4 Bond angle restraints: 14378 Sorted by residual: angle pdb=" N LEU A 154 " pdb=" CA LEU A 154 " pdb=" C LEU A 154 " ideal model delta sigma weight residual 112.23 105.62 6.61 1.26e+00 6.30e-01 2.75e+01 angle pdb=" CA GLY B 31 " pdb=" C GLY B 31 " pdb=" O GLY B 31 " ideal model delta sigma weight residual 121.66 118.07 3.59 8.80e-01 1.29e+00 1.66e+01 angle pdb=" CA ASP A 149 " pdb=" CB ASP A 149 " pdb=" CG ASP A 149 " ideal model delta sigma weight residual 112.60 116.28 -3.68 1.00e+00 1.00e+00 1.36e+01 angle pdb=" CA GLY A 228 " pdb=" C GLY A 228 " pdb=" O GLY A 228 " ideal model delta sigma weight residual 120.40 116.96 3.44 1.08e+00 8.57e-01 1.02e+01 angle pdb=" N THR A 226 " pdb=" CA THR A 226 " pdb=" C THR A 226 " ideal model delta sigma weight residual 112.54 108.73 3.81 1.22e+00 6.72e-01 9.76e+00 ... (remaining 14373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 6067 29.37 - 58.75: 194 58.75 - 88.12: 37 88.12 - 117.49: 8 117.49 - 146.86: 3 Dihedral angle restraints: 6309 sinusoidal: 2533 harmonic: 3776 Sorted by residual: dihedral pdb=" C19 6OU B 603 " pdb=" C20 6OU B 603 " pdb=" C21 6OU B 603 " pdb=" O22 6OU B 603 " ideal model delta sinusoidal sigma weight residual 301.00 154.14 146.86 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C19 6OU B 602 " pdb=" C16 6OU B 602 " pdb=" O18 6OU B 602 " pdb=" O17 6OU B 602 " ideal model delta sinusoidal sigma weight residual 6.39 -137.74 144.13 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C15 6OU B 602 " pdb=" C16 6OU B 602 " pdb=" O18 6OU B 602 " pdb=" C19 6OU B 602 " ideal model delta sinusoidal sigma weight residual 175.68 -42.21 -142.11 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 6306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1359 0.050 - 0.100: 242 0.100 - 0.150: 31 0.150 - 0.200: 5 0.200 - 0.250: 2 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CA ILE A 227 " pdb=" N ILE A 227 " pdb=" C ILE A 227 " pdb=" CB ILE A 227 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 227 " pdb=" CA ILE A 227 " pdb=" CG1 ILE A 227 " pdb=" CG2 ILE A 227 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 1636 not shown) Planarity restraints: 1823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 649 " 0.023 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP A 649 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 649 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 649 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 649 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 649 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 649 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 649 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 649 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 649 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 150 " -0.289 9.50e-02 1.11e+02 1.29e-01 1.03e+01 pdb=" NE ARG A 150 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 150 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 150 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 150 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 203 " -0.016 2.00e-02 2.50e+03 1.25e-02 2.75e+00 pdb=" CG PHE A 203 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 203 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 203 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 203 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 203 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 203 " -0.004 2.00e-02 2.50e+03 ... (remaining 1820 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1798 2.77 - 3.30: 9911 3.30 - 3.83: 18411 3.83 - 4.37: 23307 4.37 - 4.90: 39115 Nonbonded interactions: 92542 Sorted by model distance: nonbonded pdb=" O ASP A 648 " pdb=" O HOH A1001 " model vdw 2.232 3.040 nonbonded pdb=" O ALA A 535 " pdb=" O HOH A1002 " model vdw 2.236 3.040 nonbonded pdb=" O LEU A 658 " pdb=" ND2 ASN A 661 " model vdw 2.241 3.120 nonbonded pdb=" NH1 ARG A 387 " pdb=" OE2 GLU A 390 " model vdw 2.242 3.120 nonbonded pdb=" O GLY B 355 " pdb=" O HOH B 701 " model vdw 2.245 3.040 ... (remaining 92537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10613 Z= 0.192 Angle : 0.522 6.878 14378 Z= 0.298 Chirality : 0.039 0.250 1639 Planarity : 0.005 0.129 1823 Dihedral : 16.012 146.862 3869 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 0.57 % Allowed : 0.19 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1307 helix: 1.63 (0.19), residues: 813 sheet: -0.16 (0.57), residues: 78 loop : -0.13 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 823 TYR 0.012 0.001 TYR B 34 PHE 0.028 0.001 PHE A 203 TRP 0.066 0.002 TRP A 649 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (10610) covalent geometry : angle 0.52227 / 0.30 (14378) hydrogen bonds : bond 0.14444 / 9.62 ( 638) hydrogen bonds : angle 5.71174 / 4.02 ( 1863) metal coordination : bond 0.00267 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.484 Fit side-chains REVERT: A 75 ASP cc_start: 0.6968 (t70) cc_final: 0.6657 (t0) REVERT: A 476 GLU cc_start: 0.6602 (tp30) cc_final: 0.6397 (tp30) REVERT: A 632 GLN cc_start: 0.7740 (tt0) cc_final: 0.7401 (tt0) REVERT: B 249 MET cc_start: 0.8326 (mmt) cc_final: 0.7301 (mmt) REVERT: B 369 ASN cc_start: 0.7611 (m-40) cc_final: 0.7386 (m110) outliers start: 6 outliers final: 1 residues processed: 136 average time/residue: 0.7378 time to fit residues: 106.6578 Evaluate side-chains 110 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 189 GLN A 362 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109964 restraints weight = 10566.948| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.51 r_work: 0.3271 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10613 Z= 0.160 Angle : 0.543 7.253 14378 Z= 0.280 Chirality : 0.039 0.180 1639 Planarity : 0.005 0.042 1823 Dihedral : 11.835 146.017 1582 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 1.42 % Allowed : 4.46 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1307 helix: 1.84 (0.18), residues: 821 sheet: -0.38 (0.55), residues: 78 loop : -0.10 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 534 TYR 0.013 0.002 TYR A 172 PHE 0.027 0.002 PHE A 203 TRP 0.034 0.001 TRP A 649 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10610) covalent geometry : angle 0.54330 / 0.28 (14378) hydrogen bonds : bond 0.05069 / 3.38 ( 638) hydrogen bonds : angle 4.26623 / 3.04 ( 1863) metal coordination : bond 0.00235 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.395 Fit side-chains REVERT: A 75 ASP cc_start: 0.7045 (t70) cc_final: 0.6624 (t0) REVERT: A 210 ASN cc_start: 0.8112 (t0) cc_final: 0.7870 (t0) REVERT: A 213 GLU cc_start: 0.6965 (mp0) cc_final: 0.6740 (mp0) REVERT: A 417 GLN cc_start: 0.7462 (tt0) cc_final: 0.7137 (tt0) REVERT: A 632 GLN cc_start: 0.7919 (tt0) cc_final: 0.7555 (tt0) REVERT: A 763 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: A 764 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: B 249 MET cc_start: 0.8392 (mmt) cc_final: 0.7734 (mmt) REVERT: B 369 ASN cc_start: 0.7714 (m-40) cc_final: 0.7507 (m110) outliers start: 15 outliers final: 9 residues processed: 118 average time/residue: 0.7877 time to fit residues: 98.6280 Evaluate side-chains 110 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 129 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 7 HIS B 66 GLN B 490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111286 restraints weight = 10597.132| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.52 r_work: 0.3292 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10613 Z= 0.120 Angle : 0.483 7.093 14378 Z= 0.249 Chirality : 0.037 0.161 1639 Planarity : 0.004 0.045 1823 Dihedral : 11.235 145.697 1582 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 1.42 % Allowed : 6.26 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1307 helix: 2.03 (0.18), residues: 822 sheet: -0.49 (0.55), residues: 78 loop : -0.07 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.011 0.002 TYR B 34 PHE 0.023 0.002 PHE A 203 TRP 0.020 0.001 TRP A 649 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10610) covalent geometry : angle 0.48320 / 0.25 (14378) hydrogen bonds : bond 0.04312 / 2.88 ( 638) hydrogen bonds : angle 4.04135 / 2.88 ( 1863) metal coordination : bond 0.00124 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.339 Fit side-chains REVERT: A 75 ASP cc_start: 0.7062 (t70) cc_final: 0.6727 (t0) REVERT: A 180 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.8015 (p) REVERT: A 210 ASN cc_start: 0.8037 (t0) cc_final: 0.7793 (t0) REVERT: A 213 GLU cc_start: 0.6967 (mp0) cc_final: 0.6736 (mp0) REVERT: A 417 GLN cc_start: 0.7378 (tt0) cc_final: 0.7102 (tt0) REVERT: A 632 GLN cc_start: 0.7920 (tt0) cc_final: 0.7554 (tt0) REVERT: A 764 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: B 249 MET cc_start: 0.8351 (mmt) cc_final: 0.7477 (mmt) REVERT: B 369 ASN cc_start: 0.7708 (m-40) cc_final: 0.7493 (m110) REVERT: B 521 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6424 (mtp85) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 0.7300 time to fit residues: 87.5181 Evaluate side-chains 112 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 521 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 7 HIS B 247 GLN B 490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114463 restraints weight = 10636.407| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.52 r_work: 0.3338 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10613 Z= 0.122 Angle : 0.480 6.720 14378 Z= 0.247 Chirality : 0.037 0.160 1639 Planarity : 0.004 0.045 1823 Dihedral : 10.961 146.694 1580 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 1.99 % Allowed : 6.17 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.24), residues: 1307 helix: 2.12 (0.18), residues: 822 sheet: -0.54 (0.55), residues: 78 loop : -0.07 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.011 0.002 TYR A 172 PHE 0.020 0.002 PHE A 203 TRP 0.015 0.001 TRP A 649 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10610) covalent geometry : angle 0.48000 / 0.25 (14378) hydrogen bonds : bond 0.04221 / 2.82 ( 638) hydrogen bonds : angle 3.96189 / 2.82 ( 1863) metal coordination : bond 0.00119 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.380 Fit side-chains REVERT: A 75 ASP cc_start: 0.7105 (t70) cc_final: 0.6806 (t0) REVERT: A 180 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 210 ASN cc_start: 0.8037 (t0) cc_final: 0.7806 (t0) REVERT: A 417 GLN cc_start: 0.7352 (tt0) cc_final: 0.7070 (tt0) REVERT: A 632 GLN cc_start: 0.7954 (tt0) cc_final: 0.7573 (tt0) REVERT: A 764 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: B 249 MET cc_start: 0.8367 (mmt) cc_final: 0.7626 (mmt) REVERT: B 369 ASN cc_start: 0.7726 (m-40) cc_final: 0.7501 (m110) REVERT: B 521 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6372 (mtp85) outliers start: 21 outliers final: 12 residues processed: 118 average time/residue: 0.7027 time to fit residues: 88.2218 Evaluate side-chains 114 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 521 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 107 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 7 HIS B 490 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113860 restraints weight = 10525.367| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.51 r_work: 0.3329 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10613 Z= 0.130 Angle : 0.491 6.885 14378 Z= 0.252 Chirality : 0.038 0.160 1639 Planarity : 0.004 0.046 1823 Dihedral : 10.827 147.350 1580 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.70 % Rotamer: Outliers : 2.28 % Allowed : 6.55 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1307 helix: 2.12 (0.18), residues: 822 sheet: -0.57 (0.54), residues: 78 loop : -0.09 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.011 0.002 TYR A 172 PHE 0.019 0.002 PHE A 203 TRP 0.014 0.001 TRP A 649 HIS 0.006 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10610) covalent geometry : angle 0.49061 / 0.25 (14378) hydrogen bonds : bond 0.04339 / 2.90 ( 638) hydrogen bonds : angle 3.96701 / 2.83 ( 1863) metal coordination : bond 0.00143 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.425 Fit side-chains REVERT: A 75 ASP cc_start: 0.7162 (t70) cc_final: 0.6817 (t0) REVERT: A 180 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 210 ASN cc_start: 0.8062 (t0) cc_final: 0.7831 (t0) REVERT: A 236 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 417 GLN cc_start: 0.7354 (tt0) cc_final: 0.7040 (tt0) REVERT: A 632 GLN cc_start: 0.7974 (tt0) cc_final: 0.7590 (tt0) REVERT: A 764 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: B 249 MET cc_start: 0.8392 (mmt) cc_final: 0.7535 (mmt) REVERT: B 369 ASN cc_start: 0.7735 (m-40) cc_final: 0.7511 (m110) REVERT: B 521 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6390 (mtp85) outliers start: 24 outliers final: 14 residues processed: 121 average time/residue: 0.7384 time to fit residues: 95.1575 Evaluate side-chains 119 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 521 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 490 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111881 restraints weight = 10627.355| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.52 r_work: 0.3305 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10613 Z= 0.172 Angle : 0.543 7.868 14378 Z= 0.277 Chirality : 0.040 0.171 1639 Planarity : 0.005 0.048 1823 Dihedral : 11.090 148.602 1580 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.70 % Rotamer: Outliers : 2.28 % Allowed : 7.12 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.23), residues: 1307 helix: 1.97 (0.18), residues: 823 sheet: -0.59 (0.54), residues: 78 loop : -0.18 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 534 TYR 0.013 0.002 TYR A 172 PHE 0.019 0.002 PHE A 239 TRP 0.012 0.001 TRP A 649 HIS 0.006 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (10610) covalent geometry : angle 0.54288 / 0.28 (14378) hydrogen bonds : bond 0.04968 / 3.33 ( 638) hydrogen bonds : angle 4.06005 / 2.89 ( 1863) metal coordination : bond 0.00210 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.381 Fit side-chains REVERT: A 75 ASP cc_start: 0.7165 (t70) cc_final: 0.6844 (t0) REVERT: A 180 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 210 ASN cc_start: 0.8195 (t0) cc_final: 0.7971 (t0) REVERT: A 236 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 417 GLN cc_start: 0.7490 (tt0) cc_final: 0.7175 (tt0) REVERT: A 625 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.6584 (mtp85) REVERT: A 632 GLN cc_start: 0.7996 (tt0) cc_final: 0.7602 (tt0) REVERT: A 764 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: B 369 ASN cc_start: 0.7801 (m-40) cc_final: 0.7576 (m110) REVERT: B 521 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6540 (mtp85) outliers start: 24 outliers final: 12 residues processed: 124 average time/residue: 0.7361 time to fit residues: 97.3849 Evaluate side-chains 117 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 521 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 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 482 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 490 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114915 restraints weight = 10513.954| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.51 r_work: 0.3344 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10613 Z= 0.110 Angle : 0.467 6.869 14378 Z= 0.240 Chirality : 0.037 0.145 1639 Planarity : 0.004 0.046 1823 Dihedral : 10.661 150.248 1580 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.09 % Allowed : 7.97 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.24), residues: 1307 helix: 2.22 (0.18), residues: 822 sheet: -0.63 (0.54), residues: 78 loop : -0.07 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.010 0.001 TYR B 34 PHE 0.015 0.001 PHE A 203 TRP 0.010 0.001 TRP B 44 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (10610) covalent geometry : angle 0.46720 / 0.24 (14378) hydrogen bonds : bond 0.03992 / 2.67 ( 638) hydrogen bonds : angle 3.87347 / 2.76 ( 1863) metal coordination : bond 0.00089 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.442 Fit side-chains REVERT: A 75 ASP cc_start: 0.7119 (t70) cc_final: 0.6842 (t0) REVERT: A 180 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.8111 (p) REVERT: A 210 ASN cc_start: 0.7999 (t0) cc_final: 0.7775 (t0) REVERT: A 236 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.7624 (t80) REVERT: A 417 GLN cc_start: 0.7378 (tt0) cc_final: 0.7058 (tt0) REVERT: A 632 GLN cc_start: 0.7974 (tt0) cc_final: 0.7593 (tt0) REVERT: A 764 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7531 (pt0) REVERT: B 369 ASN cc_start: 0.7740 (m-40) cc_final: 0.7526 (m110) REVERT: B 521 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6367 (mtp85) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 0.7096 time to fit residues: 94.6429 Evaluate side-chains 119 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 521 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 71 optimal weight: 0.0000 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 482 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 247 GLN B 490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122939 restraints weight = 10578.133| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.40 r_work: 0.3425 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10613 Z= 0.090 Angle : 0.433 6.945 14378 Z= 0.223 Chirality : 0.036 0.149 1639 Planarity : 0.004 0.043 1823 Dihedral : 10.102 150.849 1580 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.61 % Allowed : 8.63 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.24), residues: 1307 helix: 2.39 (0.18), residues: 830 sheet: -0.52 (0.55), residues: 78 loop : 0.04 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.008 0.001 TYR B 34 PHE 0.014 0.001 PHE A 143 TRP 0.011 0.001 TRP B 44 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (10610) covalent geometry : angle 0.43314 / 0.22 (14378) hydrogen bonds : bond 0.03362 / 2.23 ( 638) hydrogen bonds : angle 3.68860 / 2.63 ( 1863) metal coordination : bond 0.00050 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.424 Fit side-chains REVERT: A 75 ASP cc_start: 0.7241 (t70) cc_final: 0.6940 (t0) REVERT: A 79 GLN cc_start: 0.7322 (mt0) cc_final: 0.7099 (mt0) REVERT: A 210 ASN cc_start: 0.7899 (t0) cc_final: 0.7626 (t160) REVERT: A 423 GLN cc_start: 0.8661 (mt0) cc_final: 0.8400 (mt0) REVERT: A 632 GLN cc_start: 0.8006 (tt0) cc_final: 0.7619 (tm-30) REVERT: B 369 ASN cc_start: 0.7772 (m-40) cc_final: 0.7569 (m110) outliers start: 17 outliers final: 10 residues processed: 129 average time/residue: 0.7103 time to fit residues: 97.5881 Evaluate side-chains 119 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 827 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 115 optimal weight: 0.0970 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 612 GLN A 616 GLN A 790 HIS A 817 HIS B 490 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117153 restraints weight = 10645.550| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.41 r_work: 0.3355 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10613 Z= 0.158 Angle : 0.527 7.684 14378 Z= 0.269 Chirality : 0.039 0.171 1639 Planarity : 0.004 0.046 1823 Dihedral : 10.619 151.003 1580 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.80 % Allowed : 8.82 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.23), residues: 1307 helix: 2.17 (0.18), residues: 823 sheet: -0.58 (0.55), residues: 78 loop : -0.07 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.013 0.002 TYR A 172 PHE 0.019 0.002 PHE A 239 TRP 0.010 0.001 TRP A 649 HIS 0.008 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (10610) covalent geometry : angle 0.52746 / 0.27 (14378) hydrogen bonds : bond 0.04700 / 3.14 ( 638) hydrogen bonds : angle 3.92761 / 2.80 ( 1863) metal coordination : bond 0.00177 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.394 Fit side-chains REVERT: A 75 ASP cc_start: 0.7235 (t70) cc_final: 0.6958 (t0) REVERT: A 210 ASN cc_start: 0.8081 (t0) cc_final: 0.7853 (t0) REVERT: A 417 GLN cc_start: 0.7467 (tt0) cc_final: 0.7156 (tt0) REVERT: A 599 GLN cc_start: 0.7314 (pt0) cc_final: 0.7106 (pt0) REVERT: A 632 GLN cc_start: 0.8041 (tt0) cc_final: 0.7664 (tt0) REVERT: B 369 ASN cc_start: 0.7809 (m-40) cc_final: 0.7608 (m110) REVERT: B 521 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6443 (mtp85) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 0.7352 time to fit residues: 92.4735 Evaluate side-chains 113 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 521 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 90 optimal weight: 0.0020 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 612 GLN A 616 GLN A 790 HIS ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120486 restraints weight = 10573.121| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.40 r_work: 0.3393 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10613 Z= 0.100 Angle : 0.458 7.003 14378 Z= 0.234 Chirality : 0.036 0.146 1639 Planarity : 0.004 0.044 1823 Dihedral : 10.267 152.778 1580 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.04 % Allowed : 9.68 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.24), residues: 1307 helix: 2.34 (0.18), residues: 826 sheet: -0.61 (0.54), residues: 78 loop : -0.01 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 823 TYR 0.009 0.001 TYR B 34 PHE 0.014 0.001 PHE A 143 TRP 0.011 0.001 TRP B 44 HIS 0.007 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (10610) covalent geometry : angle 0.45790 / 0.23 (14378) hydrogen bonds : bond 0.03701 / 2.47 ( 638) hydrogen bonds : angle 3.76274 / 2.68 ( 1863) metal coordination : bond 0.00099 / 0.05 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.402 Fit side-chains REVERT: A 75 ASP cc_start: 0.7232 (t70) cc_final: 0.6936 (t0) REVERT: A 210 ASN cc_start: 0.7930 (t0) cc_final: 0.7719 (t0) REVERT: A 417 GLN cc_start: 0.7375 (tt0) cc_final: 0.7086 (tt0) REVERT: A 423 GLN cc_start: 0.8636 (mt0) cc_final: 0.8396 (mt0) REVERT: A 632 GLN cc_start: 0.8018 (tt0) cc_final: 0.7645 (tt0) REVERT: B 369 ASN cc_start: 0.7789 (m-40) cc_final: 0.7587 (m110) outliers start: 11 outliers final: 10 residues processed: 118 average time/residue: 0.7041 time to fit residues: 88.7069 Evaluate side-chains 117 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 482 HIS A 790 HIS ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118280 restraints weight = 10676.764| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.41 r_work: 0.3367 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10613 Z= 0.132 Angle : 0.500 7.430 14378 Z= 0.255 Chirality : 0.038 0.163 1639 Planarity : 0.004 0.046 1823 Dihedral : 10.417 152.249 1580 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.70 % Rotamer: Outliers : 1.23 % Allowed : 9.39 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.24), residues: 1307 helix: 2.25 (0.18), residues: 823 sheet: -0.63 (0.55), residues: 78 loop : -0.05 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 823 TYR 0.012 0.002 TYR A 172 PHE 0.017 0.002 PHE A 239 TRP 0.009 0.001 TRP B 44 HIS 0.008 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10610) covalent geometry : angle 0.50028 / 0.25 (14378) hydrogen bonds : bond 0.04279 / 2.86 ( 638) hydrogen bonds : angle 3.85183 / 2.75 ( 1863) metal coordination : bond 0.00144 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3617.80 seconds wall clock time: 62 minutes 31.14 seconds (3751.14 seconds total)