Starting phenix.real_space_refine on Wed Feb 4 12:32:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgw_53149/02_2026/9qgw_53149_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgw_53149/02_2026/9qgw_53149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qgw_53149/02_2026/9qgw_53149_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgw_53149/02_2026/9qgw_53149_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qgw_53149/02_2026/9qgw_53149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgw_53149/02_2026/9qgw_53149.map" } resolution = 3.62 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= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 50 5.16 5 C 6513 2.51 5 N 1730 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2331 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 273} Chain: "B" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7834 Classifications: {'peptide': 988} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 935} Chain breaks: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.82, per 1000 atoms: 0.18 Number of scatterers: 10252 At special positions: 0 Unit cell: (87.55, 100.3, 130.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 9 15.00 O 1950 8.00 N 1730 7.00 C 6513 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: 0.69 Conformation dependent library (CDL) restraints added in 452.3 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 9 sheets defined 50.0% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4524 through 4533 Processing helix chain 'A' and resid 4559 through 4566 Processing helix chain 'A' and resid 4572 through 4586 removed outlier: 3.746A pdb=" N VAL A4583 " --> pdb=" O ALA A4579 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A4584 " --> pdb=" O GLN A4580 " (cutoff:3.500A) Processing helix chain 'A' and resid 4687 through 4699 Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 3.789A pdb=" N GLU A4708 " --> pdb=" O TYR A4705 " (cutoff:3.500A) Processing helix chain 'A' and resid 4711 through 4715 Processing helix chain 'A' and resid 4717 through 4740 removed outlier: 3.945A pdb=" N MET A4740 " --> pdb=" O VAL A4736 " (cutoff:3.500A) Processing helix chain 'A' and resid 4740 through 4746 Processing helix chain 'A' and resid 4751 through 4762 removed outlier: 3.669A pdb=" N LYS A4762 " --> pdb=" O HIS A4758 " (cutoff:3.500A) Processing helix chain 'A' and resid 4762 through 4778 removed outlier: 3.639A pdb=" N GLN A4778 " --> pdb=" O ILE A4774 " (cutoff:3.500A) Processing helix chain 'A' and resid 4779 through 4781 No H-bonds generated for 'chain 'A' and resid 4779 through 4781' Processing helix chain 'A' and resid 4786 through 4810 removed outlier: 3.634A pdb=" N GLN A4803 " --> pdb=" O ARG A4799 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A4806 " --> pdb=" O ALA A4802 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 7.008A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.608A pdb=" N GLY B 102 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.593A pdb=" N VAL B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.558A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.783A pdb=" N SER B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.594A pdb=" N GLU B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.583A pdb=" N GLU B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.915A pdb=" N SER B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 451 through 460 removed outlier: 3.727A pdb=" N ASN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.633A pdb=" N GLU B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.682A pdb=" N ILE B 517 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.564A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.463A pdb=" N THR B 551 " --> pdb=" O THR B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.563A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 615 removed outlier: 3.601A pdb=" N ARG B 615 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.545A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.545A pdb=" N LEU B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 788 Processing helix chain 'B' and resid 821 through 834 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 915 removed outlier: 3.778A pdb=" N THR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 910 " --> pdb=" O ALA B 906 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 921 removed outlier: 3.583A pdb=" N TYR B 921 " --> pdb=" O PHE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 980 Processing helix chain 'B' and resid 1002 through 1007 removed outlier: 3.719A pdb=" N LEU B1005 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1014 Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540 removed outlier: 3.567A pdb=" N ASP A4538 " --> pdb=" O VAL A4599 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A4601 " --> pdb=" O ASP A4538 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A4602 " --> pdb=" O ILE A4608 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A4608 " --> pdb=" O ASP A4602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 3.768A pdb=" N CYS B 156 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262 removed outlier: 4.688A pdb=" N PHE B 244 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE B 250 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLY B 285 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLY B 286 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 230 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B 221 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 228 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541 removed outlier: 5.818A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 496 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 563 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 564 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N SER B 591 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR B 566 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N THR B 593 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 947 removed outlier: 6.747A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.448A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B1027 " --> pdb=" O MET B 985 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET B 985 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 986 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.448A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1359 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: 1.51 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3327 1.34 - 1.46: 1716 1.46 - 1.57: 5361 1.57 - 1.69: 11 1.69 - 1.81: 73 Bond restraints: 10488 Sorted by residual: bond pdb=" CB THR B 626 " pdb=" OG1 THR B 626 " ideal model delta sigma weight residual 1.433 1.409 0.024 1.60e-02 3.91e+03 2.17e+00 bond pdb=" N THR B 626 " pdb=" CA THR B 626 " ideal model delta sigma weight residual 1.458 1.477 -0.018 1.26e-02 6.30e+03 2.06e+00 bond pdb=" CA PRO A4640 " pdb=" C PRO A4640 " ideal model delta sigma weight residual 1.517 1.508 0.009 6.70e-03 2.23e+04 1.81e+00 bond pdb=" CE2 TYR A4660 " pdb=" CZ TYR A4660 " ideal model delta sigma weight residual 1.378 1.408 -0.030 2.40e-02 1.74e+03 1.53e+00 bond pdb=" CE1 TYR A4660 " pdb=" CZ TYR A4660 " ideal model delta sigma weight residual 1.378 1.406 -0.028 2.40e-02 1.74e+03 1.41e+00 ... (remaining 10483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 14032 1.67 - 3.33: 176 3.33 - 5.00: 21 5.00 - 6.67: 2 6.67 - 8.33: 1 Bond angle restraints: 14232 Sorted by residual: angle pdb=" N CYS A4666 " pdb=" CA CYS A4666 " pdb=" CB CYS A4666 " ideal model delta sigma weight residual 110.55 102.22 8.33 1.57e+00 4.06e-01 2.82e+01 angle pdb=" C CYS A4666 " pdb=" CA CYS A4666 " pdb=" CB CYS A4666 " ideal model delta sigma weight residual 110.19 116.21 -6.02 1.64e+00 3.72e-01 1.35e+01 angle pdb=" C PHE B 624 " pdb=" N SER B 625 " pdb=" CA SER B 625 " ideal model delta sigma weight residual 120.68 126.06 -5.38 1.70e+00 3.46e-01 1.00e+01 angle pdb=" C PRO B 623 " pdb=" N PHE B 624 " pdb=" CA PHE B 624 " ideal model delta sigma weight residual 120.38 124.58 -4.20 1.37e+00 5.33e-01 9.39e+00 angle pdb=" CA GLY C 75 " pdb=" C GLY C 75 " pdb=" N ALA C 76 " ideal model delta sigma weight residual 115.33 118.66 -3.33 1.15e+00 7.56e-01 8.39e+00 ... (remaining 14227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 6043 16.65 - 33.30: 280 33.30 - 49.95: 48 49.95 - 66.61: 10 66.61 - 83.26: 7 Dihedral angle restraints: 6388 sinusoidal: 2637 harmonic: 3751 Sorted by residual: dihedral pdb=" CA MET B 69 " pdb=" C MET B 69 " pdb=" N GLY B 70 " pdb=" CA GLY B 70 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLN B 262 " pdb=" C GLN B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" N MET A4609 " pdb=" CA MET A4609 " pdb=" CB MET A4609 " pdb=" CG MET A4609 " ideal model delta sinusoidal sigma weight residual -60.00 -117.72 57.72 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 6385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 967 0.029 - 0.058: 402 0.058 - 0.086: 116 0.086 - 0.115: 93 0.115 - 0.144: 11 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA THR B 626 " pdb=" N THR B 626 " pdb=" C THR B 626 " pdb=" CB THR B 626 " both_signs ideal model delta sigma weight residual False 2.53 2.66 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 745 " pdb=" N ILE B 745 " pdb=" C ILE B 745 " pdb=" CB ILE B 745 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1586 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 624 " -0.027 2.00e-02 2.50e+03 1.66e-02 4.82e+00 pdb=" CG PHE B 624 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 624 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 624 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 624 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 624 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 624 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A4660 " -0.024 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR A4660 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR A4660 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A4660 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A4660 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A4660 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A4660 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A4660 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A4656 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A4657 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A4657 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A4657 " 0.026 5.00e-02 4.00e+02 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1477 2.76 - 3.47: 14278 3.47 - 4.19: 22082 4.19 - 4.90: 40597 Nonbonded interactions: 78436 Sorted by model distance: nonbonded pdb=" OG SER B 625 " pdb=" C ALA C 76 " model vdw 1.327 3.270 nonbonded pdb=" SG CYS A4666 " pdb=" CB ALA C 76 " model vdw 1.823 3.820 nonbonded pdb=" OG SER B 625 " pdb=" O ALA C 76 " model vdw 2.227 3.040 nonbonded pdb=" CB SER B 625 " pdb=" C ALA C 76 " model vdw 2.476 3.670 nonbonded pdb=" OG SER B 625 " pdb=" CA ALA C 76 " model vdw 2.498 3.470 ... (remaining 78431 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 group one per residue 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.460 Find NCS groups from input model: 0.030 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 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 0.043 10488 Z= 0.168 Angle : 0.491 8.334 14232 Z= 0.264 Chirality : 0.040 0.144 1589 Planarity : 0.003 0.046 1822 Dihedral : 10.387 83.257 3952 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.80 % Allowed : 4.24 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.23 (0.25), residues: 1274 helix: 2.68 (0.23), residues: 537 sheet: 1.23 (0.40), residues: 190 loop : 0.41 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4576 TYR 0.024 0.001 TYR A4660 PHE 0.027 0.001 PHE B 624 TRP 0.013 0.001 TRP A4673 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00367 (10488) covalent geometry : angle 0.49052 (14232) hydrogen bonds : bond 0.18817 ( 493) hydrogen bonds : angle 6.03851 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.393 Fit side-chains REVERT: A 4542 MET cc_start: 0.9363 (mtt) cc_final: 0.9139 (mpp) REVERT: B 401 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8319 (tp30) REVERT: B 594 MET cc_start: 0.9030 (tmm) cc_final: 0.8335 (tmm) REVERT: B 844 MET cc_start: 0.8594 (ttm) cc_final: 0.8325 (ttm) REVERT: B 985 MET cc_start: 0.8839 (ptm) cc_final: 0.8442 (ppp) outliers start: 9 outliers final: 3 residues processed: 35 average time/residue: 0.0810 time to fit residues: 4.3711 Evaluate side-chains 27 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 791 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4758 HIS B 47 GLN B 262 GLN ** B 858 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 = 0.2914 r_free = 0.2914 target = 0.034378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.025831 restraints weight = 75013.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026757 restraints weight = 41501.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.027408 restraints weight = 28776.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.027851 restraints weight = 22697.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028144 restraints weight = 19387.228| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10488 Z= 0.120 Angle : 0.450 5.107 14232 Z= 0.239 Chirality : 0.039 0.161 1589 Planarity : 0.003 0.045 1822 Dihedral : 5.208 78.935 1451 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.35 % Allowed : 5.57 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.33 (0.25), residues: 1274 helix: 2.71 (0.23), residues: 543 sheet: 1.46 (0.40), residues: 184 loop : 0.44 (0.29), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.008 0.001 TYR A4621 PHE 0.009 0.001 PHE B 464 TRP 0.008 0.001 TRP B 660 HIS 0.003 0.000 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00261 (10488) covalent geometry : angle 0.44987 (14232) hydrogen bonds : bond 0.04130 ( 493) hydrogen bonds : angle 4.47803 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.250 Fit side-chains REVERT: A 4532 MET cc_start: 0.9486 (tpp) cc_final: 0.9016 (mmm) REVERT: A 4542 MET cc_start: 0.9317 (mtt) cc_final: 0.9110 (mpp) REVERT: B 162 MET cc_start: 0.8946 (mmm) cc_final: 0.8739 (mmm) REVERT: B 253 MET cc_start: 0.9219 (mtp) cc_final: 0.9007 (mtt) REVERT: B 449 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8519 (m) REVERT: B 492 MET cc_start: 0.8475 (tpp) cc_final: 0.8112 (tpp) REVERT: B 594 MET cc_start: 0.8978 (tmm) cc_final: 0.8402 (tmm) REVERT: B 844 MET cc_start: 0.8585 (ttm) cc_final: 0.8274 (ttm) REVERT: B 985 MET cc_start: 0.8735 (ptm) cc_final: 0.8407 (ppp) REVERT: B 1009 MET cc_start: 0.8959 (tpp) cc_final: 0.8313 (mmm) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.0683 time to fit residues: 3.1904 Evaluate side-chains 25 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 495 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4671 ASN ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4778 GLN B 599 HIS ** B 858 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 = 0.2898 r_free = 0.2898 target = 0.034098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.025506 restraints weight = 76226.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.026422 restraints weight = 42380.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027057 restraints weight = 29535.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.027484 restraints weight = 23475.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.027750 restraints weight = 20150.938| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10488 Z= 0.138 Angle : 0.443 5.722 14232 Z= 0.232 Chirality : 0.039 0.142 1589 Planarity : 0.003 0.044 1822 Dihedral : 5.004 77.637 1445 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.53 % Allowed : 6.19 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.36 (0.25), residues: 1274 helix: 2.77 (0.23), residues: 545 sheet: 1.40 (0.40), residues: 184 loop : 0.42 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 691 TYR 0.009 0.001 TYR A4621 PHE 0.009 0.001 PHE B 183 TRP 0.009 0.001 TRP B 660 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00305 (10488) covalent geometry : angle 0.44293 (14232) hydrogen bonds : bond 0.03671 ( 493) hydrogen bonds : angle 4.14692 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.390 Fit side-chains REVERT: A 4532 MET cc_start: 0.9512 (tpp) cc_final: 0.9292 (tpp) REVERT: A 4542 MET cc_start: 0.9377 (mtt) cc_final: 0.9108 (mpp) REVERT: B 162 MET cc_start: 0.8915 (mmm) cc_final: 0.8702 (mmm) REVERT: B 253 MET cc_start: 0.9232 (mtp) cc_final: 0.9018 (mtt) REVERT: B 449 CYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 594 MET cc_start: 0.9002 (tmm) cc_final: 0.8449 (tmm) REVERT: B 844 MET cc_start: 0.8649 (ttm) cc_final: 0.8214 (ttm) REVERT: B 985 MET cc_start: 0.8791 (ptm) cc_final: 0.8419 (ppp) REVERT: B 1009 MET cc_start: 0.9043 (tpp) cc_final: 0.8427 (mmm) outliers start: 6 outliers final: 1 residues processed: 29 average time/residue: 0.0681 time to fit residues: 3.4511 Evaluate side-chains 25 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 495 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 26 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.034213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025729 restraints weight = 75655.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.026656 restraints weight = 41350.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.027309 restraints weight = 28517.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.027747 restraints weight = 22460.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.028022 restraints weight = 19166.835| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10488 Z= 0.105 Angle : 0.428 7.993 14232 Z= 0.222 Chirality : 0.039 0.142 1589 Planarity : 0.003 0.043 1822 Dihedral : 4.892 77.167 1445 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.62 % Allowed : 6.28 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.44 (0.25), residues: 1274 helix: 2.84 (0.23), residues: 547 sheet: 1.44 (0.40), residues: 184 loop : 0.46 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 691 TYR 0.007 0.001 TYR B 979 PHE 0.009 0.001 PHE B 183 TRP 0.008 0.001 TRP B 660 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00234 (10488) covalent geometry : angle 0.42803 (14232) hydrogen bonds : bond 0.03141 ( 493) hydrogen bonds : angle 3.97304 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.302 Fit side-chains REVERT: A 4542 MET cc_start: 0.9326 (mtt) cc_final: 0.9109 (mpp) REVERT: B 162 MET cc_start: 0.8853 (mmm) cc_final: 0.8628 (mmm) REVERT: B 253 MET cc_start: 0.9211 (mtp) cc_final: 0.8990 (mtt) REVERT: B 594 MET cc_start: 0.8972 (tmm) cc_final: 0.8473 (tmm) REVERT: B 844 MET cc_start: 0.8659 (ttm) cc_final: 0.8203 (ttm) REVERT: B 985 MET cc_start: 0.8784 (ptm) cc_final: 0.8444 (ppp) REVERT: B 1009 MET cc_start: 0.8988 (tpp) cc_final: 0.8480 (mmm) outliers start: 7 outliers final: 1 residues processed: 30 average time/residue: 0.0526 time to fit residues: 2.8062 Evaluate side-chains 24 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.033826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.025284 restraints weight = 75202.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.026199 restraints weight = 41984.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.026844 restraints weight = 29144.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.027264 restraints weight = 23022.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.027550 restraints weight = 19709.368| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10488 Z= 0.128 Angle : 0.444 7.974 14232 Z= 0.228 Chirality : 0.039 0.147 1589 Planarity : 0.003 0.043 1822 Dihedral : 4.863 76.532 1445 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.62 % Allowed : 6.90 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.42 (0.25), residues: 1274 helix: 2.81 (0.23), residues: 546 sheet: 1.29 (0.40), residues: 189 loop : 0.52 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A4805 TYR 0.008 0.001 TYR A4621 PHE 0.009 0.001 PHE B 183 TRP 0.008 0.001 TRP B 660 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00288 (10488) covalent geometry : angle 0.44427 (14232) hydrogen bonds : bond 0.03270 ( 493) hydrogen bonds : angle 3.95145 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.298 Fit side-chains REVERT: A 4542 MET cc_start: 0.9324 (mtt) cc_final: 0.9103 (mpp) REVERT: B 162 MET cc_start: 0.8883 (mmm) cc_final: 0.8625 (mmm) REVERT: B 253 MET cc_start: 0.9202 (mtp) cc_final: 0.8968 (mtt) REVERT: B 594 MET cc_start: 0.8964 (tmm) cc_final: 0.8471 (tmm) REVERT: B 844 MET cc_start: 0.8679 (ttm) cc_final: 0.8270 (ttm) REVERT: B 985 MET cc_start: 0.8808 (ptm) cc_final: 0.8447 (ppp) REVERT: B 1009 MET cc_start: 0.8961 (tpp) cc_final: 0.8554 (mmm) outliers start: 7 outliers final: 3 residues processed: 30 average time/residue: 0.0913 time to fit residues: 4.3249 Evaluate side-chains 26 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 791 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025559 restraints weight = 75830.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.026483 restraints weight = 41542.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.027122 restraints weight = 28816.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.027546 restraints weight = 22777.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.027827 restraints weight = 19511.216| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10488 Z= 0.097 Angle : 0.415 6.991 14232 Z= 0.214 Chirality : 0.038 0.141 1589 Planarity : 0.003 0.042 1822 Dihedral : 4.752 76.157 1445 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.35 % Allowed : 7.25 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.43 (0.25), residues: 1274 helix: 2.83 (0.23), residues: 547 sheet: 1.30 (0.39), residues: 192 loop : 0.50 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 175 TYR 0.007 0.001 TYR B 979 PHE 0.009 0.001 PHE B 183 TRP 0.007 0.001 TRP B 660 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00217 (10488) covalent geometry : angle 0.41475 (14232) hydrogen bonds : bond 0.02907 ( 493) hydrogen bonds : angle 3.84316 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.322 Fit side-chains REVERT: A 4542 MET cc_start: 0.9323 (mtt) cc_final: 0.9087 (mpp) REVERT: B 253 MET cc_start: 0.9204 (mtp) cc_final: 0.8995 (mtt) REVERT: B 594 MET cc_start: 0.8956 (tmm) cc_final: 0.8515 (tmm) REVERT: B 844 MET cc_start: 0.8672 (ttm) cc_final: 0.8264 (ttm) REVERT: B 985 MET cc_start: 0.8800 (ptm) cc_final: 0.8445 (ppp) REVERT: B 1009 MET cc_start: 0.8944 (tpp) cc_final: 0.8532 (mmm) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.0641 time to fit residues: 3.1069 Evaluate side-chains 26 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 124 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 overall best weight: 2.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.024960 restraints weight = 76667.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.025858 restraints weight = 42192.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.026489 restraints weight = 29303.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.026902 restraints weight = 23206.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.027193 restraints weight = 19930.655| |-----------------------------------------------------------------------------| r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10488 Z= 0.169 Angle : 0.477 8.708 14232 Z= 0.241 Chirality : 0.039 0.135 1589 Planarity : 0.003 0.043 1822 Dihedral : 4.851 76.760 1445 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.44 % Allowed : 7.78 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.38 (0.25), residues: 1274 helix: 2.81 (0.23), residues: 547 sheet: 1.22 (0.39), residues: 189 loop : 0.47 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 175 TYR 0.009 0.001 TYR A4621 PHE 0.009 0.001 PHE B 183 TRP 0.008 0.001 TRP B 660 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00378 (10488) covalent geometry : angle 0.47658 (14232) hydrogen bonds : bond 0.03397 ( 493) hydrogen bonds : angle 3.98514 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.458 Fit side-chains REVERT: A 4542 MET cc_start: 0.9346 (mtt) cc_final: 0.9086 (mpp) REVERT: B 253 MET cc_start: 0.9220 (mtp) cc_final: 0.8993 (mtt) REVERT: B 594 MET cc_start: 0.8977 (tmm) cc_final: 0.8504 (tmm) REVERT: B 844 MET cc_start: 0.8685 (ttm) cc_final: 0.8170 (ttm) REVERT: B 985 MET cc_start: 0.8846 (ptm) cc_final: 0.8440 (ppp) REVERT: B 1009 MET cc_start: 0.8991 (tpp) cc_final: 0.8593 (mmm) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.0978 time to fit residues: 4.7118 Evaluate side-chains 26 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 791 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.025239 restraints weight = 77406.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.026139 restraints weight = 42826.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026786 restraints weight = 29758.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.027207 restraints weight = 23520.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.027483 restraints weight = 20117.988| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10488 Z= 0.147 Angle : 0.453 7.887 14232 Z= 0.232 Chirality : 0.039 0.137 1589 Planarity : 0.003 0.043 1822 Dihedral : 4.842 76.731 1445 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.44 % Allowed : 7.96 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.39 (0.25), residues: 1274 helix: 2.83 (0.23), residues: 547 sheet: 1.22 (0.39), residues: 188 loop : 0.46 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.008 0.001 TYR A4621 PHE 0.009 0.001 PHE B 183 TRP 0.009 0.001 TRP B 660 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00330 (10488) covalent geometry : angle 0.45254 (14232) hydrogen bonds : bond 0.03275 ( 493) hydrogen bonds : angle 3.95055 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.449 Fit side-chains REVERT: A 4542 MET cc_start: 0.9386 (mtt) cc_final: 0.9081 (mpp) REVERT: B 253 MET cc_start: 0.9220 (mtp) cc_final: 0.8983 (mtt) REVERT: B 594 MET cc_start: 0.8998 (tmm) cc_final: 0.8569 (tmm) REVERT: B 844 MET cc_start: 0.8655 (ttm) cc_final: 0.8150 (ttm) REVERT: B 985 MET cc_start: 0.8878 (ptm) cc_final: 0.8445 (ppp) REVERT: B 1009 MET cc_start: 0.9016 (tpp) cc_final: 0.8576 (mmm) outliers start: 5 outliers final: 2 residues processed: 30 average time/residue: 0.0963 time to fit residues: 4.8268 Evaluate side-chains 25 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 113 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025964 restraints weight = 75881.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.026891 restraints weight = 41784.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.027540 restraints weight = 28964.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027964 restraints weight = 22866.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028240 restraints weight = 19529.532| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10488 Z= 0.078 Angle : 0.422 8.414 14232 Z= 0.216 Chirality : 0.038 0.140 1589 Planarity : 0.003 0.042 1822 Dihedral : 4.680 75.806 1445 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.35 % Allowed : 7.87 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.44 (0.25), residues: 1274 helix: 2.80 (0.23), residues: 548 sheet: 1.45 (0.39), residues: 187 loop : 0.49 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.009 0.001 TYR B 979 PHE 0.010 0.001 PHE B 183 TRP 0.008 0.001 TRP B 660 HIS 0.002 0.000 HIS A4758 Details of bonding type rmsd covalent geometry : bond 0.00169 (10488) covalent geometry : angle 0.42208 (14232) hydrogen bonds : bond 0.02756 ( 493) hydrogen bonds : angle 3.77112 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.446 Fit side-chains REVERT: A 4542 MET cc_start: 0.9374 (mtt) cc_final: 0.9064 (mpp) REVERT: B 59 MET cc_start: 0.8903 (mtm) cc_final: 0.8664 (mtm) REVERT: B 253 MET cc_start: 0.9194 (mtp) cc_final: 0.8988 (mtt) REVERT: B 594 MET cc_start: 0.8975 (tmm) cc_final: 0.8526 (tmm) REVERT: B 844 MET cc_start: 0.8689 (ttm) cc_final: 0.8261 (ttm) REVERT: B 985 MET cc_start: 0.8813 (ptm) cc_final: 0.8479 (ppp) REVERT: B 1009 MET cc_start: 0.8981 (tpp) cc_final: 0.8550 (mmm) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0843 time to fit residues: 4.1232 Evaluate side-chains 25 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 0.0570 chunk 55 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.034878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.026458 restraints weight = 75157.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.027396 restraints weight = 41409.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.028046 restraints weight = 28716.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028476 restraints weight = 22673.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.028747 restraints weight = 19338.188| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10488 Z= 0.074 Angle : 0.415 8.507 14232 Z= 0.212 Chirality : 0.038 0.139 1589 Planarity : 0.003 0.041 1822 Dihedral : 4.514 74.905 1445 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.18 % Allowed : 8.05 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.47 (0.25), residues: 1274 helix: 2.83 (0.23), residues: 547 sheet: 1.33 (0.40), residues: 193 loop : 0.57 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.008 0.001 TYR B 979 PHE 0.010 0.001 PHE B 183 TRP 0.006 0.001 TRP B 378 HIS 0.002 0.000 HIS A4800 Details of bonding type rmsd covalent geometry : bond 0.00162 (10488) covalent geometry : angle 0.41538 (14232) hydrogen bonds : bond 0.02439 ( 493) hydrogen bonds : angle 3.66111 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.459 Fit side-chains REVERT: A 4542 MET cc_start: 0.9360 (mtt) cc_final: 0.9059 (mpp) REVERT: A 4740 MET cc_start: 0.8860 (mtt) cc_final: 0.8177 (mmt) REVERT: B 59 MET cc_start: 0.8897 (mtm) cc_final: 0.8646 (mtm) REVERT: B 594 MET cc_start: 0.8972 (tmm) cc_final: 0.8553 (tmm) REVERT: B 844 MET cc_start: 0.8667 (ttm) cc_final: 0.8298 (ttm) REVERT: B 985 MET cc_start: 0.8782 (ptm) cc_final: 0.8465 (ppp) REVERT: B 1009 MET cc_start: 0.8958 (tpp) cc_final: 0.8517 (mmm) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.0839 time to fit residues: 3.9222 Evaluate side-chains 25 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.034518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.026076 restraints weight = 76137.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.027008 restraints weight = 41967.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.027656 restraints weight = 29107.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.028071 restraints weight = 22996.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.028360 restraints weight = 19676.735| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10488 Z= 0.086 Angle : 0.421 8.523 14232 Z= 0.214 Chirality : 0.038 0.138 1589 Planarity : 0.003 0.040 1822 Dihedral : 4.495 75.226 1445 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.18 % Allowed : 7.96 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % 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: 2.51 (0.25), residues: 1274 helix: 2.85 (0.23), residues: 547 sheet: 1.41 (0.40), residues: 191 loop : 0.56 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.006 0.001 TYR B 979 PHE 0.010 0.001 PHE B 183 TRP 0.006 0.001 TRP A4673 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00194 (10488) covalent geometry : angle 0.42094 (14232) hydrogen bonds : bond 0.02586 ( 493) hydrogen bonds : angle 3.66174 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.47 seconds wall clock time: 24 minutes 40.65 seconds (1480.65 seconds total)