Starting phenix.real_space_refine on Mon Jul 28 07:26:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u58_26344/07_2025/7u58_26344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u58_26344/07_2025/7u58_26344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u58_26344/07_2025/7u58_26344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u58_26344/07_2025/7u58_26344.map" model { file = "/net/cci-nas-00/data/ceres_data/7u58_26344/07_2025/7u58_26344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u58_26344/07_2025/7u58_26344.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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 2 6.06 5 Mg 4 5.21 5 S 35 5.16 5 C 6428 2.51 5 N 1720 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10087 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5096 Classifications: {'peptide': 651} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 42, 'TRANS': 608} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4985 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 41, 'TRANS': 599} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 140 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 926 SG CYS A 199 35.164 50.440 68.066 1.00 67.92 S ATOM 955 SG CYS A 202 36.831 50.109 64.634 1.00 63.64 S ATOM 1483 SG CYS A 318 33.090 49.817 65.028 1.00 71.34 S ATOM 1502 SG CYS A 321 34.757 53.185 65.361 1.00 72.28 S ATOM 5928 SG CYS B 199 86.874 33.955 67.864 1.00 68.02 S ATOM 5957 SG CYS B 202 85.323 34.538 64.297 1.00 66.02 S ATOM 6470 SG CYS B 318 89.018 34.744 64.923 1.00 70.34 S ATOM 6489 SG CYS B 321 87.253 31.368 65.168 1.00 73.53 S Time building chain proxies: 6.78, per 1000 atoms: 0.67 Number of scatterers: 10087 At special positions: 0 Unit cell: (123.318, 84.32, 103.292, 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 2 29.99 S 35 16.00 Mg 4 11.99 O 1898 8.00 N 1720 7.00 C 6428 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: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 318 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 202 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 199 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 321 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 318 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 321 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 199 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 202 " Number of angles added : 12 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 41.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.909A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.621A pdb=" N GLN A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.630A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 removed outlier: 4.112A pdb=" N ASN A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.800A pdb=" N LEU A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 206 " --> pdb=" O CYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.532A pdb=" N VAL A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.934A pdb=" N ARG A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 467 through 473 removed outlier: 3.588A pdb=" N TYR A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.665A pdb=" N ARG A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 543 through 568 removed outlier: 3.537A pdb=" N ASN A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.882A pdb=" N LEU A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 651 removed outlier: 3.631A pdb=" N ILE A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 691 through 695 removed outlier: 4.035A pdb=" N TYR A 695 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 717 removed outlier: 3.689A pdb=" N ASP A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 762 removed outlier: 4.225A pdb=" N TYR A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Proline residue: A 759 - end of helix Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.783A pdb=" N GLN B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 removed outlier: 3.597A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 173 removed outlier: 4.030A pdb=" N LYS B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.917A pdb=" N LEU B 203 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 284 removed outlier: 3.606A pdb=" N GLN B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.684A pdb=" N GLU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.856A pdb=" N TYR B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 437 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.569A pdb=" N LEU B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.600A pdb=" N CYS B 463 " --> pdb=" O HIS B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 543 through 567 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.829A pdb=" N LEU B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 652 removed outlier: 4.361A pdb=" N ILE B 650 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 651 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 652 " --> pdb=" O ASN B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 662 removed outlier: 3.760A pdb=" N GLU B 662 " --> pdb=" O VAL B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 673 removed outlier: 4.016A pdb=" N GLU B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 691 through 695 removed outlier: 3.915A pdb=" N TYR B 695 " --> pdb=" O TYR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 717 removed outlier: 3.555A pdb=" N ALA B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 762 removed outlier: 4.148A pdb=" N TYR B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Proline residue: B 759 - end of helix Processing helix chain 'B' and resid 770 through 774 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 136 removed outlier: 5.957A pdb=" N VAL A 110 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLN A 109 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL A 151 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A 111 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 153 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER A 113 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU A 177 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 150 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 179 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 152 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 448 Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 448 removed outlier: 6.251A pdb=" N ASP A 725 " --> pdb=" O PRO A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 602 Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.457A pdb=" N GLN B 109 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL B 151 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 111 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU B 153 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER B 113 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU B 177 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 150 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE B 179 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 152 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 448 Processing sheet with id=AB1, first strand: chain 'B' and resid 446 through 448 removed outlier: 6.187A pdb=" N ASP B 725 " --> pdb=" O PRO B 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 596 through 602 384 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3331 1.34 - 1.46: 2269 1.46 - 1.58: 4677 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 10325 Sorted by residual: bond pdb=" C THR B 288 " pdb=" N PRO B 289 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.21e+00 bond pdb=" C THR A 288 " pdb=" N PRO A 289 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.03e-01 bond pdb=" CB PRO B 289 " pdb=" CG PRO B 289 " ideal model delta sigma weight residual 1.492 1.528 -0.036 5.00e-02 4.00e+02 5.22e-01 bond pdb=" CG GLU B 128 " pdb=" CD GLU B 128 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.86e-01 bond pdb=" CA GLU B 128 " pdb=" CB GLU B 128 " ideal model delta sigma weight residual 1.529 1.541 -0.012 1.74e-02 3.30e+03 4.79e-01 ... (remaining 10320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 13800 1.46 - 2.92: 242 2.92 - 4.39: 51 4.39 - 5.85: 13 5.85 - 7.31: 1 Bond angle restraints: 14107 Sorted by residual: angle pdb=" N GLU B 128 " pdb=" CA GLU B 128 " pdb=" CB GLU B 128 " ideal model delta sigma weight residual 110.39 115.41 -5.02 1.66e+00 3.63e-01 9.14e+00 angle pdb=" N GLU B 712 " pdb=" CA GLU B 712 " pdb=" CB GLU B 712 " ideal model delta sigma weight residual 110.28 114.54 -4.26 1.55e+00 4.16e-01 7.56e+00 angle pdb=" C GLU B 658 " pdb=" N VAL B 659 " pdb=" CA VAL B 659 " ideal model delta sigma weight residual 121.97 126.85 -4.88 1.80e+00 3.09e-01 7.36e+00 angle pdb=" CB MET A 708 " pdb=" CG MET A 708 " pdb=" SD MET A 708 " ideal model delta sigma weight residual 112.70 120.01 -7.31 3.00e+00 1.11e-01 5.94e+00 angle pdb=" C LEU B 127 " pdb=" N GLU B 128 " pdb=" CA GLU B 128 " ideal model delta sigma weight residual 120.72 116.74 3.98 1.67e+00 3.59e-01 5.68e+00 ... (remaining 14102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 5535 16.62 - 33.25: 532 33.25 - 49.87: 109 49.87 - 66.49: 14 66.49 - 83.11: 10 Dihedral angle restraints: 6200 sinusoidal: 2415 harmonic: 3785 Sorted by residual: dihedral pdb=" CA ASP B 730 " pdb=" CB ASP B 730 " pdb=" CG ASP B 730 " pdb=" OD1 ASP B 730 " ideal model delta sinusoidal sigma weight residual -30.00 -87.85 57.85 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CG ARG B 315 " pdb=" CD ARG B 315 " pdb=" NE ARG B 315 " pdb=" CZ ARG B 315 " ideal model delta sinusoidal sigma weight residual -180.00 -135.18 -44.82 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA TYR A 746 " pdb=" C TYR A 746 " pdb=" N TRP A 747 " pdb=" CA TRP A 747 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 967 0.030 - 0.060: 417 0.060 - 0.090: 121 0.090 - 0.120: 91 0.120 - 0.150: 13 Chirality restraints: 1609 Sorted by residual: chirality pdb=" CA THR B 288 " pdb=" N THR B 288 " pdb=" C THR B 288 " pdb=" CB THR B 288 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE B 513 " pdb=" N ILE B 513 " pdb=" C ILE B 513 " pdb=" CB ILE B 513 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE B 601 " pdb=" N ILE B 601 " pdb=" C ILE B 601 " pdb=" CB ILE B 601 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1606 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 318 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 319 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 740 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 741 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 741 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 741 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 180 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO B 181 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.019 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 155 2.66 - 3.22: 9651 3.22 - 3.78: 15733 3.78 - 4.34: 21430 4.34 - 4.90: 34975 Nonbonded interactions: 81944 Sorted by model distance: nonbonded pdb=" OE1 GLU A 554 " pdb="MG MG A 802 " model vdw 2.098 2.170 nonbonded pdb=" OE1 GLU B 554 " pdb="MG MG B 802 " model vdw 2.101 2.170 nonbonded pdb=" OE2 GLU B 554 " pdb="MG MG B 802 " model vdw 2.176 2.170 nonbonded pdb=" OE2 GLU A 554 " pdb="MG MG A 802 " model vdw 2.202 2.170 nonbonded pdb=" O PRO A 289 " pdb=" NH2 ARG B 303 " model vdw 2.239 3.120 ... (remaining 81939 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 91 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 101 or (resid 102 through 103 and \ (name N or name CA or name C or name O or name CB )) or resid 104 through 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 7 through 111 or (resid 112 and (name N or name CA or name C or name O or name C \ B )) or resid 113 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 208 or (resid 209 and (name N or name \ CA or name C or name O or name CB )) or resid 210 through 213 or resid 264 throu \ gh 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) or \ resid 291 through 368 or (resid 369 and (name N or name CA or name C or name O \ or name CB )) or resid 370 through 373 or (resid 374 and (name N or name CA or n \ ame C or name O or name CB )) or resid 375 or (resid 376 and (name N or name CA \ or name C or name O or name CB )) or resid 377 through 393 or (resid 394 and (na \ me N or name CA or name C or name O or name CB )) or resid 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 411 o \ r (resid 412 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 13 through 570 or (resid 571 and (name N or name CA or name C or name O or name \ CB )) or resid 572 through 601 or (resid 602 and (name N or name CA or name C or \ name O or name CB )) or resid 603 through 703 or (resid 704 and (name N or name \ CA or name C or name O or name CB )) or resid 705 through 707 or (resid 708 and \ (name N or name CA or name C or name O or name CB )) or resid 709 through 746 o \ r (resid 747 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 48 through 781 or resid 801 through 803)) selection = (chain 'B' and (resid 91 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB )) or resid 129 through 291 or (resid 292 through 293 a \ nd (name N or name CA or name C or name O or name CB )) or resid 294 through 381 \ or (resid 382 and (name N or name CA or name C or name O or name CB )) or resid \ 383 through 417 or (resid 418 and (name N or name CA or name C or name O or nam \ e CB )) or resid 419 through 423 or (resid 424 through 425 and (name N or name C \ A or name C or name O or name CB )) or resid 426 through 439 or (resid 440 and ( \ name N or name CA or name C or name O or name CB )) or resid 441 through 455 or \ (resid 456 through 457 and (name N or name CA or name C or name O or name CB )) \ or resid 458 through 472 or (resid 473 and (name N or name CA or name C or name \ O or name CB )) or resid 474 through 475 or (resid 476 and (name N or name CA or \ name C or name O or name CB )) or resid 477 through 510 or (resid 511 and (name \ N or name CA or name C or name O or name CB )) or resid 512 through 541 or (res \ id 542 through 543 and (name N or name CA or name C or name O or name CB )) or r \ esid 544 through 645 or (resid 646 and (name N or name CA or name C or name O or \ name CB )) or resid 647 through 648 or (resid 649 and (name N or name CA or nam \ e C or name O or name CB )) or resid 650 through 744 or (resid 745 and (name N o \ r name CA or name C or name O or name CB )) or resid 746 through 781 or resid 80 \ 1 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.160 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.003 0.036 10333 Z= 0.108 Angle : 0.516 7.310 14119 Z= 0.260 Chirality : 0.042 0.150 1609 Planarity : 0.004 0.042 1828 Dihedral : 13.759 83.113 3744 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1284 helix: 1.04 (0.27), residues: 408 sheet: 0.02 (0.39), residues: 177 loop : -0.15 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 747 HIS 0.003 0.001 HIS A 269 PHE 0.012 0.001 PHE A 428 TYR 0.020 0.001 TYR A 157 ARG 0.004 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.15847 ( 376) hydrogen bonds : angle 5.94529 ( 1029) metal coordination : bond 0.00561 ( 8) metal coordination : angle 2.45228 ( 12) covalent geometry : bond 0.00251 (10325) covalent geometry : angle 0.51077 (14107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 538 ASP cc_start: 0.7498 (t0) cc_final: 0.7239 (t0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2021 time to fit residues: 17.1294 Evaluate side-chains 42 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 0.0970 chunk 101 optimal weight: 0.0060 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086457 restraints weight = 20295.571| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.07 r_work: 0.3201 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10333 Z= 0.109 Angle : 0.519 8.462 14119 Z= 0.260 Chirality : 0.043 0.140 1609 Planarity : 0.004 0.041 1828 Dihedral : 3.599 14.655 1386 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 0.37 % Allowed : 5.17 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1284 helix: 1.27 (0.26), residues: 427 sheet: 0.16 (0.38), residues: 184 loop : -0.22 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 200 HIS 0.004 0.001 HIS A 269 PHE 0.014 0.001 PHE A 663 TYR 0.018 0.001 TYR B 746 ARG 0.004 0.000 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 376) hydrogen bonds : angle 4.32080 ( 1029) metal coordination : bond 0.00656 ( 8) metal coordination : angle 2.17692 ( 12) covalent geometry : bond 0.00259 (10325) covalent geometry : angle 0.51518 (14107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 538 ASP cc_start: 0.8157 (t0) cc_final: 0.7701 (t0) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.2537 time to fit residues: 20.4336 Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 29 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 0.0040 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 109 GLN B 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.113777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084922 restraints weight = 20548.137| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.07 r_work: 0.3175 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10333 Z= 0.118 Angle : 0.507 6.401 14119 Z= 0.253 Chirality : 0.043 0.145 1609 Planarity : 0.004 0.043 1828 Dihedral : 3.561 15.937 1386 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 0.83 % Allowed : 8.13 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1284 helix: 1.45 (0.26), residues: 427 sheet: 0.20 (0.38), residues: 185 loop : -0.22 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS A 269 PHE 0.011 0.001 PHE A 428 TYR 0.021 0.001 TYR B 746 ARG 0.003 0.000 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 376) hydrogen bonds : angle 4.04292 ( 1029) metal coordination : bond 0.00750 ( 8) metal coordination : angle 2.22105 ( 12) covalent geometry : bond 0.00284 (10325) covalent geometry : angle 0.50272 (14107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 538 ASP cc_start: 0.8297 (t0) cc_final: 0.7807 (t0) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.2324 time to fit residues: 21.9621 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.114467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085953 restraints weight = 20434.407| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.03 r_work: 0.3204 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.002 0.034 10333 Z= 0.101 Angle : 0.500 5.953 14119 Z= 0.250 Chirality : 0.043 0.140 1609 Planarity : 0.004 0.041 1828 Dihedral : 3.500 15.290 1386 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 0.83 % Allowed : 10.53 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1284 helix: 1.52 (0.26), residues: 427 sheet: 0.24 (0.38), residues: 185 loop : -0.20 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.003 0.001 HIS A 269 PHE 0.010 0.001 PHE A 428 TYR 0.018 0.001 TYR B 746 ARG 0.002 0.000 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 376) hydrogen bonds : angle 3.91414 ( 1029) metal coordination : bond 0.00606 ( 8) metal coordination : angle 2.06029 ( 12) covalent geometry : bond 0.00243 (10325) covalent geometry : angle 0.49676 (14107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8201 (t80) cc_final: 0.7858 (t80) REVERT: A 452 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: A 538 ASP cc_start: 0.8342 (t0) cc_final: 0.7772 (t0) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.2174 time to fit residues: 17.6691 Evaluate side-chains 54 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 108 optimal weight: 0.0270 chunk 111 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.113609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.085655 restraints weight = 20698.679| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.08 r_work: 0.3219 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10333 Z= 0.113 Angle : 0.498 6.072 14119 Z= 0.248 Chirality : 0.043 0.145 1609 Planarity : 0.004 0.042 1828 Dihedral : 3.487 15.463 1386 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 1.48 % Allowed : 11.17 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1284 helix: 1.61 (0.26), residues: 427 sheet: 0.23 (0.38), residues: 185 loop : -0.23 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS A 269 PHE 0.012 0.001 PHE B 663 TYR 0.021 0.001 TYR B 746 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 376) hydrogen bonds : angle 3.83176 ( 1029) metal coordination : bond 0.00710 ( 8) metal coordination : angle 2.08616 ( 12) covalent geometry : bond 0.00273 (10325) covalent geometry : angle 0.49407 (14107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8238 (t80) cc_final: 0.7881 (t80) REVERT: A 264 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6943 (pp) outliers start: 16 outliers final: 5 residues processed: 58 average time/residue: 0.2646 time to fit residues: 23.3016 Evaluate side-chains 48 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 118 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.085357 restraints weight = 20468.991| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.18 r_work: 0.3173 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10333 Z= 0.097 Angle : 0.490 6.466 14119 Z= 0.244 Chirality : 0.042 0.140 1609 Planarity : 0.003 0.040 1828 Dihedral : 3.417 15.144 1386 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.02 % Allowed : 12.47 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1284 helix: 1.64 (0.26), residues: 428 sheet: 0.30 (0.39), residues: 185 loop : -0.20 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS A 269 PHE 0.010 0.001 PHE A 428 TYR 0.018 0.001 TYR B 746 ARG 0.001 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.02833 ( 376) hydrogen bonds : angle 3.75039 ( 1029) metal coordination : bond 0.00589 ( 8) metal coordination : angle 1.90637 ( 12) covalent geometry : bond 0.00235 (10325) covalent geometry : angle 0.48682 (14107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8259 (t80) cc_final: 0.7937 (t80) REVERT: A 264 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6687 (pp) REVERT: A 452 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: B 185 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8675 (mm) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.2257 time to fit residues: 18.7779 Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 712 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 119 optimal weight: 0.0870 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.113879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085405 restraints weight = 20656.229| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.01 r_work: 0.3171 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10333 Z= 0.106 Angle : 0.494 6.525 14119 Z= 0.246 Chirality : 0.043 0.148 1609 Planarity : 0.003 0.040 1828 Dihedral : 3.411 15.214 1386 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 1.57 % Allowed : 12.93 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1284 helix: 1.67 (0.26), residues: 428 sheet: 0.30 (0.39), residues: 185 loop : -0.19 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS A 269 PHE 0.013 0.001 PHE B 663 TYR 0.019 0.001 TYR B 746 ARG 0.001 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 376) hydrogen bonds : angle 3.72968 ( 1029) metal coordination : bond 0.00660 ( 8) metal coordination : angle 1.95328 ( 12) covalent geometry : bond 0.00258 (10325) covalent geometry : angle 0.49125 (14107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8253 (t80) cc_final: 0.7969 (t80) REVERT: A 264 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6931 (pp) REVERT: B 473 TYR cc_start: 0.8600 (m-10) cc_final: 0.8305 (m-10) outliers start: 17 outliers final: 9 residues processed: 54 average time/residue: 0.3043 time to fit residues: 26.6842 Evaluate side-chains 51 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 712 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.113852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.086177 restraints weight = 20799.905| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.02 r_work: 0.3202 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10333 Z= 0.117 Angle : 0.506 6.657 14119 Z= 0.252 Chirality : 0.043 0.149 1609 Planarity : 0.003 0.041 1828 Dihedral : 3.460 15.538 1386 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 1.11 % Allowed : 13.67 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1284 helix: 1.70 (0.26), residues: 425 sheet: 0.29 (0.39), residues: 185 loop : -0.19 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 200 HIS 0.004 0.001 HIS A 269 PHE 0.016 0.001 PHE B 663 TYR 0.020 0.001 TYR B 746 ARG 0.003 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 376) hydrogen bonds : angle 3.74494 ( 1029) metal coordination : bond 0.00716 ( 8) metal coordination : angle 1.98788 ( 12) covalent geometry : bond 0.00283 (10325) covalent geometry : angle 0.50290 (14107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8298 (t80) cc_final: 0.8065 (t80) REVERT: A 264 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6997 (pp) REVERT: B 473 TYR cc_start: 0.8575 (m-10) cc_final: 0.8291 (m-10) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.3570 time to fit residues: 27.5192 Evaluate side-chains 48 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 712 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.113470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.085785 restraints weight = 20772.772| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.00 r_work: 0.3187 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10333 Z= 0.127 Angle : 0.516 6.875 14119 Z= 0.257 Chirality : 0.043 0.146 1609 Planarity : 0.003 0.041 1828 Dihedral : 3.514 16.131 1386 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 1.29 % Allowed : 13.67 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1284 helix: 1.70 (0.26), residues: 425 sheet: 0.26 (0.39), residues: 185 loop : -0.19 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 91 HIS 0.004 0.001 HIS A 269 PHE 0.011 0.001 PHE A 428 TYR 0.021 0.001 TYR B 746 ARG 0.006 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 376) hydrogen bonds : angle 3.77339 ( 1029) metal coordination : bond 0.00780 ( 8) metal coordination : angle 2.16372 ( 12) covalent geometry : bond 0.00308 (10325) covalent geometry : angle 0.51254 (14107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6885 (pp) REVERT: B 473 TYR cc_start: 0.8669 (m-10) cc_final: 0.8377 (m-10) outliers start: 14 outliers final: 11 residues processed: 51 average time/residue: 0.3219 time to fit residues: 25.5926 Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 746 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 0.0070 chunk 93 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.113498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084560 restraints weight = 20509.530| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.25 r_work: 0.3190 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10333 Z= 0.105 Angle : 0.504 7.241 14119 Z= 0.251 Chirality : 0.043 0.147 1609 Planarity : 0.003 0.040 1828 Dihedral : 3.472 15.575 1386 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 0.92 % Allowed : 14.04 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1284 helix: 1.72 (0.26), residues: 425 sheet: 0.09 (0.38), residues: 195 loop : -0.13 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS A 269 PHE 0.011 0.001 PHE B 663 TYR 0.019 0.001 TYR B 746 ARG 0.005 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.02887 ( 376) hydrogen bonds : angle 3.73142 ( 1029) metal coordination : bond 0.00652 ( 8) metal coordination : angle 2.03552 ( 12) covalent geometry : bond 0.00253 (10325) covalent geometry : angle 0.50037 (14107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6844 (pp) REVERT: B 430 GLU cc_start: 0.8013 (tt0) cc_final: 0.7680 (tt0) REVERT: B 473 TYR cc_start: 0.8631 (m-10) cc_final: 0.8334 (m-10) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.2066 time to fit residues: 16.3020 Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 712 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 15 optimal weight: 0.0070 chunk 85 optimal weight: 8.9990 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.114010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.086179 restraints weight = 20626.614| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.06 r_work: 0.3229 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10333 Z= 0.101 Angle : 0.498 7.263 14119 Z= 0.248 Chirality : 0.043 0.148 1609 Planarity : 0.003 0.040 1828 Dihedral : 3.438 15.410 1386 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 1.11 % Allowed : 14.04 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1284 helix: 1.81 (0.26), residues: 421 sheet: 0.11 (0.38), residues: 195 loop : -0.04 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS A 623 PHE 0.010 0.001 PHE A 428 TYR 0.018 0.001 TYR B 746 ARG 0.006 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 376) hydrogen bonds : angle 3.70812 ( 1029) metal coordination : bond 0.00621 ( 8) metal coordination : angle 1.98200 ( 12) covalent geometry : bond 0.00243 (10325) covalent geometry : angle 0.49523 (14107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5249.53 seconds wall clock time: 97 minutes 0.56 seconds (5820.56 seconds total)