Starting phenix.real_space_refine on Fri Sep 11 14:15:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.map" model { file = "/net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zg1_11191/09_2026/6zg1_11191.cif" } resolution = 3.77 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 6232 2.51 5 N 1769 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9931 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1164 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 143, 1164 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} bond proxies already assigned to first conformer: 1132 Chain: "B" Number of atoms: 1324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1250 Chain: "C" Number of atoms: 1232 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1206 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 142} Conformer: "B" Number of residues, atoms: 148, 1206 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 142} bond proxies already assigned to first conformer: 1199 Chain: "D" Number of atoms: 1204 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} bond proxies already assigned to first conformer: 1200 Chain: "E" Number of atoms: 1209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} bond proxies already assigned to first conformer: 1196 Chain: "F" Number of atoms: 1211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1174 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 144, 1174 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} bond proxies already assigned to first conformer: 1152 Chain: "G" Number of atoms: 1206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 1181 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 145, 1181 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} bond proxies already assigned to first conformer: 1174 Chain: "H" Number of atoms: 1210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 140} Conformer: "B" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 140} bond proxies already assigned to first conformer: 1189 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {'BME': 1, 'EDO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {'BME': 1, 'EDO': 4, 'PEG': 1, 'PGE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 16 Unusual residues: {'BME': 1, 'EDO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 35 Unusual residues: {'BME': 1, 'EDO': 6, 'PEG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BME': 1, 'EDO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BME': 1, 'EDO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BME': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BME': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" C1 BME A 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME A 602 " occ=0.60 residue: pdb=" C1 EDO B 602 " occ=0.80 ... (2 atoms not shown) pdb=" O2 EDO B 602 " occ=0.80 residue: pdb=" C1 PEG B 603 " occ=0.80 ... (5 atoms not shown) pdb=" O4 PEG B 603 " occ=0.80 residue: pdb=" C1 BME B 604 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME B 604 " occ=0.60 residue: pdb=" C1 PGE B 605 " occ=0.70 ... (8 atoms not shown) pdb=" O4 PGE B 605 " occ=0.70 residue: pdb=" C1 BME C 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME C 601 " occ=0.60 residue: pdb=" C1 PEG D 602 " occ=0.80 ... (5 atoms not shown) pdb=" O4 PEG D 602 " occ=0.80 residue: pdb=" C1 BME D 603 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME D 603 " occ=0.60 residue: pdb=" C1 EDO D 606 " occ=0.80 ... (2 atoms not shown) pdb=" O2 EDO D 606 " occ=0.80 residue: pdb=" C1 BME E 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME E 602 " occ=0.60 residue: pdb=" C1 BME F 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME F 602 " occ=0.60 residue: pdb=" C1 BME G 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME G 601 " occ=0.60 residue: pdb=" C1 BME H 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME H 601 " occ=0.60 Time building chain proxies: 3.92, per 1000 atoms: 0.39 Number of scatterers: 9931 At special positions: 0 Unit cell: (121, 119.9, 69.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1866 8.00 N 1769 7.00 C 6232 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 634.0 milliseconds 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.547A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.733A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.731A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 4.450A pdb=" N HIS A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 544 Processing helix chain 'B' and resid 394 through 398 removed outlier: 3.655A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.669A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.634A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 4.451A pdb=" N HIS B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 544 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 476 Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.517A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.523A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.667A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.455A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 544 removed outlier: 3.973A pdb=" N GLU C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 477 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.515A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.867A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.757A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 518 removed outlier: 4.715A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 544 removed outlier: 3.527A pdb=" N GLU D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 459 through 476 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.509A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.621A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.683A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 4.548A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 544 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 436 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 459 through 477 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.521A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.735A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.704A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 removed outlier: 4.441A pdb=" N HIS F 516 " --> pdb=" O ARG F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 544 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 459 through 476 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.524A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.714A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.716A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 516 removed outlier: 4.382A pdb=" N HIS G 516 " --> pdb=" O ARG G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 544 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 439 through 445 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 459 through 477 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.515A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.672A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.667A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 516 removed outlier: 4.435A pdb=" N HIS H 516 " --> pdb=" O ARG H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.656A pdb=" N GLU H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1327 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: 1.35 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1912 1.32 - 1.46: 3330 1.46 - 1.59: 4810 1.59 - 1.72: 0 1.72 - 1.85: 80 Bond restraints: 10132 Sorted by residual: bond pdb=" C LEU F 406 " pdb=" O LEU F 406 " ideal model delta sigma weight residual 1.234 1.218 0.016 5.00e-03 4.00e+04 1.08e+01 bond pdb=" CA SER H 480 " pdb=" CB SER H 480 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.56e-02 4.11e+03 8.85e+00 bond pdb=" CG ASP H 439 " pdb=" OD2 ASP H 439 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.82e+00 bond pdb=" CA GLY C 504 " pdb=" C GLY C 504 " ideal model delta sigma weight residual 1.515 1.548 -0.033 1.15e-02 7.56e+03 8.30e+00 bond pdb=" CG ASP G 439 " pdb=" OD2 ASP G 439 " ideal model delta sigma weight residual 1.249 1.194 0.055 1.90e-02 2.77e+03 8.30e+00 ... (remaining 10127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 13227 3.66 - 7.31: 393 7.31 - 10.97: 36 10.97 - 14.62: 7 14.62 - 18.28: 1 Bond angle restraints: 13664 Sorted by residual: angle pdb=" CB GLU D 414 " pdb=" CG GLU D 414 " pdb=" CD GLU D 414 " ideal model delta sigma weight residual 112.60 130.88 -18.28 1.70e+00 3.46e-01 1.16e+02 angle pdb=" C CYS B 508 " pdb=" CA CYS B 508 " pdb=" CB CYS B 508 " ideal model delta sigma weight residual 110.01 96.31 13.70 1.80e+00 3.09e-01 5.79e+01 angle pdb=" CB GLU C 431 " pdb=" CG GLU C 431 " pdb=" CD GLU C 431 " ideal model delta sigma weight residual 112.60 125.45 -12.85 1.70e+00 3.46e-01 5.71e+01 angle pdb=" N MET A 545 " pdb=" CA MET A 545 " pdb=" C MET A 545 " ideal model delta sigma weight residual 113.50 105.29 8.21 1.23e+00 6.61e-01 4.46e+01 angle pdb=" CB BGLU B 472 " pdb=" CG BGLU B 472 " pdb=" CD BGLU B 472 " ideal model delta sigma weight residual 112.60 123.46 -10.86 1.70e+00 3.46e-01 4.08e+01 ... (remaining 13659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5972 35.95 - 71.90: 217 71.90 - 107.85: 35 107.85 - 143.80: 1 143.80 - 179.75: 2 Dihedral angle restraints: 6227 sinusoidal: 2657 harmonic: 3570 Sorted by residual: dihedral pdb=" CD BARG H 465 " pdb=" NE BARG H 465 " pdb=" CZ BARG H 465 " pdb=" NH1BARG H 465 " ideal model delta sinusoidal sigma weight residual 0.00 -179.75 179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG A 465 " pdb=" NE BARG A 465 " pdb=" CZ BARG A 465 " pdb=" NH1BARG A 465 " ideal model delta sinusoidal sigma weight residual 0.00 178.20 -178.20 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C ARG B 497 " pdb=" N ARG B 497 " pdb=" CA ARG B 497 " pdb=" CB ARG B 497 " ideal model delta harmonic sigma weight residual -122.60 -140.37 17.77 0 2.50e+00 1.60e-01 5.06e+01 ... (remaining 6224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1187 0.134 - 0.268: 282 0.268 - 0.402: 12 0.402 - 0.536: 1 0.536 - 0.670: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CA ARG B 497 " pdb=" N ARG B 497 " pdb=" C ARG B 497 " pdb=" CB ARG B 497 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA GLU H 544 " pdb=" N GLU H 544 " pdb=" C GLU H 544 " pdb=" CB GLU H 544 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA GLU H 416 " pdb=" N GLU H 416 " pdb=" C GLU H 416 " pdb=" CB GLU H 416 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 1481 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 476 " 0.046 2.00e-02 2.50e+03 2.83e-02 1.41e+01 pdb=" CG PHE E 476 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 476 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE E 476 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 476 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE E 476 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E 476 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 466 " 0.041 2.00e-02 2.50e+03 2.70e-02 1.27e+01 pdb=" CG PHE F 466 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE F 466 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE F 466 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE F 466 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 466 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE F 466 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 476 " 0.040 2.00e-02 2.50e+03 2.67e-02 1.25e+01 pdb=" CG PHE C 476 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 476 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 476 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 476 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE C 476 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 476 " 0.008 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4080 2.94 - 3.43: 10012 3.43 - 3.92: 17293 3.92 - 4.41: 20364 4.41 - 4.90: 31927 Nonbonded interactions: 83676 Sorted by model distance: nonbonded pdb=" N TYR D 479 " pdb=" O1 PEG D 602 " model vdw 2.449 3.120 nonbonded pdb=" NH2 ARG D 465 " pdb=" O1 EDO D 601 " model vdw 2.457 3.120 nonbonded pdb=" OD1 ASP G 489 " pdb=" NH1BARG G 499 " model vdw 2.457 3.120 nonbonded pdb=" OG SER F 459 " pdb=" NE2 GLN G 436 " model vdw 2.458 3.120 nonbonded pdb=" N MET A 545 " pdb=" N LEU A 546 " model vdw 2.478 2.560 ... (remaining 83671 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 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'B' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'C' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'D' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'E' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'F' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'G' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'H' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=0.97 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: 0.210 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 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 : 0.010 0.086 10140 Z= 0.638 Angle : 1.608 18.276 13664 Z= 1.047 Chirality : 0.105 0.670 1484 Planarity : 0.007 0.047 1767 Dihedral : 18.758 179.752 3939 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.98 % Favored : 97.93 % Rotamer: Outliers : 5.94 % Allowed : 6.58 % Favored : 87.49 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.21), residues: 1201 helix: -1.21 (0.16), residues: 768 sheet: None (None), residues: 0 loop : -0.26 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG F 468 TYR 0.041 0.009 TYR D 429 PHE 0.046 0.009 PHE E 476 TRP 0.034 0.008 TRP C 420 HIS 0.015 0.004 HIS E 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.62 (10132) covalent geometry : angle 1.60849 / 1.05 (13664) hydrogen bonds : bond 0.19833 / 13.33 ( 485) hydrogen bonds : angle 6.68849 / 4.87 ( 1327) Misc. bond : bond 0.05001 / 2.59 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 593 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.4846 (OUTLIER) cc_final: 0.4345 (mm) REVERT: A 411 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.6795 (t) REVERT: A 424 ILE cc_start: 0.7374 (pt) cc_final: 0.6991 (pt) REVERT: B 411 SER cc_start: 0.6983 (OUTLIER) cc_final: 0.6696 (t) REVERT: C 447 THR cc_start: 0.7911 (p) cc_final: 0.7700 (p) REVERT: D 424 ILE cc_start: 0.7058 (pt) cc_final: 0.6573 (pt) REVERT: D 473 LEU cc_start: 0.7960 (tp) cc_final: 0.7751 (tp) REVERT: D 476 PHE cc_start: 0.7518 (m-80) cc_final: 0.7313 (m-10) REVERT: E 431 GLU cc_start: 0.7646 (tp30) cc_final: 0.7418 (tt0) REVERT: E 486 ASN cc_start: 0.7796 (t0) cc_final: 0.7479 (t0) REVERT: F 447 THR cc_start: 0.8170 (p) cc_final: 0.7720 (p) REVERT: F 524 LEU cc_start: 0.7482 (tp) cc_final: 0.7228 (tt) REVERT: G 411 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7446 (t) REVERT: G 424 ILE cc_start: 0.7777 (pt) cc_final: 0.7364 (pt) REVERT: H 431 GLU cc_start: 0.8665 (tt0) cc_final: 0.8237 (tm-30) outliers start: 54 outliers final: 8 residues processed: 618 average time/residue: 0.1295 time to fit residues: 103.4109 Evaluate side-chains 386 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 374 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain H residue 416 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN B 423 GLN B 500 GLN B 530 HIS C 423 GLN B C 530 HIS ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 HIS D 418 GLN D 516 HIS ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS E 534 HIS F 422 GLN ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS G 422 GLN G 436 GLN H 423 GLN H 452 GLN H 500 GLN H 530 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.136565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.095107 restraints weight = 140821.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.103416 restraints weight = 37748.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.109450 restraints weight = 19236.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.113777 restraints weight = 12007.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.116865 restraints weight = 8362.236| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (8 function evaluations) r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10140 Z= 0.217 Angle : 0.862 9.843 13664 Z= 0.446 Chirality : 0.046 0.151 1484 Planarity : 0.006 0.064 1767 Dihedral : 10.030 178.171 1477 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.30 % Allowed : 22.56 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.24), residues: 1201 helix: -0.25 (0.18), residues: 771 sheet: None (None), residues: 0 loop : 0.96 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 517 TYR 0.029 0.003 TYR E 501 PHE 0.024 0.002 PHE B 476 TRP 0.017 0.002 TRP C 490 HIS 0.010 0.002 HIS E 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (10132) covalent geometry : angle 0.86207 / 0.45 (13664) hydrogen bonds : bond 0.05863 / 3.75 ( 485) hydrogen bonds : angle 5.29138 / 3.82 ( 1327) Misc. bond : bond 0.00158 / 0.08 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 416 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5436 (mm) REVERT: A 411 SER cc_start: 0.8168 (m) cc_final: 0.7783 (t) REVERT: A 414 GLU cc_start: 0.8786 (mp0) cc_final: 0.8416 (mp0) REVERT: A 416 GLU cc_start: 0.9375 (mp0) cc_final: 0.9113 (mp0) REVERT: A 435 GLU cc_start: 0.9517 (tm-30) cc_final: 0.9279 (pp20) REVERT: A 472 GLU cc_start: 0.8523 (tp30) cc_final: 0.8162 (tp30) REVERT: A 503 TYR cc_start: 0.8696 (t80) cc_final: 0.8475 (t80) REVERT: A 525 GLU cc_start: 0.9094 (mp0) cc_final: 0.8888 (mp0) REVERT: B 435 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9208 (pp20) REVERT: B 438 VAL cc_start: 0.8242 (t) cc_final: 0.7956 (m) REVERT: B 449 GLU cc_start: 0.8538 (tp30) cc_final: 0.8281 (tp30) REVERT: B 479 TYR cc_start: 0.8262 (m-80) cc_final: 0.7765 (m-10) REVERT: B 489 ASP cc_start: 0.9045 (m-30) cc_final: 0.8762 (t0) REVERT: B 490 TRP cc_start: 0.8201 (t-100) cc_final: 0.7826 (t-100) REVERT: B 503 TYR cc_start: 0.8245 (t80) cc_final: 0.7863 (t80) REVERT: B 520 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7091 (tm-30) REVERT: C 479 TYR cc_start: 0.7974 (m-80) cc_final: 0.7505 (m-80) REVERT: C 484 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8771 (tmm160) REVERT: C 520 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 525 GLU cc_start: 0.8904 (mp0) cc_final: 0.8462 (mp0) REVERT: D 412 TRP cc_start: 0.7649 (m-10) cc_final: 0.7110 (m-10) REVERT: D 431 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8075 (tm-30) REVERT: D 444 LEU cc_start: 0.8704 (mt) cc_final: 0.8455 (mt) REVERT: D 472 GLU cc_start: 0.8311 (tp30) cc_final: 0.7779 (tp30) REVERT: D 476 PHE cc_start: 0.8783 (m-80) cc_final: 0.7952 (m-10) REVERT: D 497 ARG cc_start: 0.8535 (mtm110) cc_final: 0.8314 (ptm160) REVERT: D 531 LEU cc_start: 0.6294 (tp) cc_final: 0.6063 (tp) REVERT: E 435 GLU cc_start: 0.9599 (tm-30) cc_final: 0.9311 (pp20) REVERT: E 438 VAL cc_start: 0.8445 (t) cc_final: 0.8144 (m) REVERT: E 449 GLU cc_start: 0.8637 (tp30) cc_final: 0.8312 (tp30) REVERT: E 503 TYR cc_start: 0.8340 (t80) cc_final: 0.8048 (t80) REVERT: F 476 PHE cc_start: 0.9155 (m-80) cc_final: 0.8796 (m-10) REVERT: F 479 TYR cc_start: 0.8056 (m-80) cc_final: 0.7785 (m-80) REVERT: G 414 GLU cc_start: 0.8493 (mp0) cc_final: 0.8263 (mm-30) REVERT: G 418 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8975 (tp40) REVERT: G 447 THR cc_start: 0.8141 (p) cc_final: 0.7771 (p) REVERT: G 476 PHE cc_start: 0.9092 (m-80) cc_final: 0.8542 (m-10) REVERT: G 479 TYR cc_start: 0.8108 (m-80) cc_final: 0.7857 (m-80) REVERT: G 503 TYR cc_start: 0.8637 (t80) cc_final: 0.8423 (t80) REVERT: G 522 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7409 (mm-40) REVERT: G 543 ARG cc_start: 0.8844 (mtt180) cc_final: 0.8281 (mtm110) REVERT: G 544 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7897 (mm-30) REVERT: G 545 MET cc_start: 0.7233 (ptp) cc_final: 0.6979 (ptt) REVERT: H 431 GLU cc_start: 0.9133 (tt0) cc_final: 0.8918 (tm-30) REVERT: H 447 THR cc_start: 0.7881 (p) cc_final: 0.6615 (p) REVERT: H 545 MET cc_start: 0.6020 (ptt) cc_final: 0.5377 (ptt) outliers start: 47 outliers final: 28 residues processed: 436 average time/residue: 0.1183 time to fit residues: 68.5210 Evaluate side-chains 375 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 346 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 530 HIS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 71 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN B 530 HIS C 436 GLN C 500 GLN C 516 HIS ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS F 530 HIS H 452 GLN H 530 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.135441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096757 restraints weight = 142486.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.104438 restraints weight = 37039.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.110087 restraints weight = 18847.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.114051 restraints weight = 11649.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.116977 restraints weight = 8051.643| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.3987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10140 Z= 0.166 Angle : 0.843 11.073 13664 Z= 0.422 Chirality : 0.046 0.187 1484 Planarity : 0.005 0.056 1767 Dihedral : 9.304 179.576 1460 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.20 % Allowed : 26.12 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1201 helix: 0.02 (0.18), residues: 773 sheet: None (None), residues: 0 loop : 0.93 (0.34), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 517 TYR 0.019 0.003 TYR E 501 PHE 0.022 0.002 PHE B 476 TRP 0.026 0.002 TRP D 490 HIS 0.013 0.002 HIS B 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (10132) covalent geometry : angle 0.84304 / 0.42 (13664) hydrogen bonds : bond 0.05088 / 3.27 ( 485) hydrogen bonds : angle 5.06798 / 3.64 ( 1327) Misc. bond : bond 0.00087 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 391 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.5994 (OUTLIER) cc_final: 0.5622 (mm) REVERT: A 411 SER cc_start: 0.8118 (m) cc_final: 0.7765 (t) REVERT: A 414 GLU cc_start: 0.8769 (mp0) cc_final: 0.8275 (mm-30) REVERT: A 416 GLU cc_start: 0.9332 (mp0) cc_final: 0.9091 (mp0) REVERT: A 435 GLU cc_start: 0.9484 (tm-30) cc_final: 0.9151 (pp20) REVERT: A 472 GLU cc_start: 0.8391 (tp30) cc_final: 0.8179 (tp30) REVERT: A 478 ASN cc_start: 0.8723 (t0) cc_final: 0.8462 (t0) REVERT: A 503 TYR cc_start: 0.8678 (t80) cc_final: 0.8249 (t80) REVERT: A 522 GLN cc_start: 0.8499 (mm-40) cc_final: 0.7825 (mm-40) REVERT: B 435 GLU cc_start: 0.9554 (tm-30) cc_final: 0.9177 (pp20) REVERT: B 438 VAL cc_start: 0.8161 (t) cc_final: 0.7839 (m) REVERT: B 457 MET cc_start: 0.6539 (mtp) cc_final: 0.6163 (ttm) REVERT: B 479 TYR cc_start: 0.8175 (m-80) cc_final: 0.7745 (m-10) REVERT: B 489 ASP cc_start: 0.9117 (m-30) cc_final: 0.8811 (t0) REVERT: B 490 TRP cc_start: 0.8190 (t-100) cc_final: 0.7817 (t-100) REVERT: B 503 TYR cc_start: 0.8314 (t80) cc_final: 0.7899 (t80) REVERT: C 468 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6991 (mtm-85) REVERT: C 474 LYS cc_start: 0.8986 (mttm) cc_final: 0.8757 (mmtt) REVERT: C 479 TYR cc_start: 0.7983 (m-80) cc_final: 0.7510 (m-80) REVERT: C 484 ARG cc_start: 0.9017 (ttm110) cc_final: 0.8725 (tmm160) REVERT: C 521 GLN cc_start: 0.8201 (pp30) cc_final: 0.7868 (pp30) REVERT: C 525 GLU cc_start: 0.8850 (mp0) cc_final: 0.8560 (mp0) REVERT: D 414 GLU cc_start: 0.9201 (mp0) cc_final: 0.8756 (mp0) REVERT: D 431 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8064 (tm-30) REVERT: D 449 GLU cc_start: 0.8764 (pp20) cc_final: 0.8445 (pp20) REVERT: D 472 GLU cc_start: 0.8306 (tp30) cc_final: 0.7723 (tp30) REVERT: D 476 PHE cc_start: 0.8739 (m-80) cc_final: 0.7870 (m-10) REVERT: D 484 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7996 (ttp80) REVERT: D 497 ARG cc_start: 0.8434 (mtm110) cc_final: 0.8129 (ptp-170) REVERT: D 517 ARG cc_start: 0.9359 (mmm-85) cc_final: 0.9127 (mmm160) REVERT: E 435 GLU cc_start: 0.9550 (tm-30) cc_final: 0.9326 (pp20) REVERT: E 449 GLU cc_start: 0.8539 (tp30) cc_final: 0.8240 (tp30) REVERT: E 474 LYS cc_start: 0.8950 (mttt) cc_final: 0.8746 (mttp) REVERT: E 503 TYR cc_start: 0.8099 (t80) cc_final: 0.7864 (t80) REVERT: F 413 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8584 (tmtt) REVERT: F 414 GLU cc_start: 0.8844 (mp0) cc_final: 0.8384 (mm-30) REVERT: F 426 PHE cc_start: 0.6357 (m-80) cc_final: 0.5995 (m-10) REVERT: F 457 MET cc_start: 0.6856 (mtt) cc_final: 0.6418 (mtp) REVERT: F 479 TYR cc_start: 0.7908 (m-80) cc_final: 0.7527 (m-80) REVERT: G 503 TYR cc_start: 0.8778 (t80) cc_final: 0.8451 (t80) REVERT: G 522 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7507 (mm-40) REVERT: G 543 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8199 (mtm110) REVERT: H 418 GLN cc_start: 0.8816 (mm110) cc_final: 0.8312 (mm110) REVERT: H 457 MET cc_start: 0.6927 (mtp) cc_final: 0.6717 (ttm) REVERT: H 545 MET cc_start: 0.5817 (ptt) cc_final: 0.5347 (ptt) outliers start: 35 outliers final: 21 residues processed: 410 average time/residue: 0.1219 time to fit residues: 66.0766 Evaluate side-chains 371 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 348 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 530 HIS Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.2980 chunk 104 optimal weight: 0.0870 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.0270 chunk 105 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 GLN A 452 GLN B 423 GLN C 436 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.133994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.092806 restraints weight = 164303.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100665 restraints weight = 40588.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.106522 restraints weight = 20723.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.110615 restraints weight = 12943.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.113583 restraints weight = 9061.996| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10140 Z= 0.164 Angle : 0.832 14.832 13664 Z= 0.415 Chirality : 0.045 0.191 1484 Planarity : 0.005 0.065 1767 Dihedral : 9.070 179.916 1460 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.74 % Allowed : 28.04 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1201 helix: 0.06 (0.18), residues: 770 sheet: None (None), residues: 0 loop : 0.67 (0.34), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 535 TYR 0.023 0.002 TYR E 501 PHE 0.021 0.001 PHE G 476 TRP 0.012 0.001 TRP D 490 HIS 0.016 0.002 HIS B 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10132) covalent geometry : angle 0.83169 / 0.42 (13664) hydrogen bonds : bond 0.04736 / 3.04 ( 485) hydrogen bonds : angle 5.10424 / 3.65 ( 1327) Misc. bond : bond 0.00064 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 372 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.6586 (OUTLIER) cc_final: 0.6280 (mm) REVERT: A 411 SER cc_start: 0.8059 (m) cc_final: 0.7799 (t) REVERT: A 414 GLU cc_start: 0.8775 (mp0) cc_final: 0.8254 (mp0) REVERT: A 450 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8373 (pt0) REVERT: A 454 ASP cc_start: 0.7332 (m-30) cc_final: 0.7074 (t0) REVERT: A 472 GLU cc_start: 0.8362 (tp30) cc_final: 0.7735 (tp30) REVERT: A 476 PHE cc_start: 0.8483 (m-10) cc_final: 0.8054 (m-10) REVERT: A 478 ASN cc_start: 0.8709 (t0) cc_final: 0.8329 (t0) REVERT: A 503 TYR cc_start: 0.8649 (t80) cc_final: 0.8272 (t80) REVERT: A 522 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7623 (mm-40) REVERT: A 525 GLU cc_start: 0.9060 (mp0) cc_final: 0.8765 (mp0) REVERT: A 529 ILE cc_start: 0.8193 (mt) cc_final: 0.7834 (tt) REVERT: A 530 HIS cc_start: 0.8632 (m90) cc_final: 0.8299 (m-70) REVERT: B 413 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8520 (tmtt) REVERT: B 435 GLU cc_start: 0.9559 (tm-30) cc_final: 0.8992 (pp20) REVERT: B 438 VAL cc_start: 0.8341 (t) cc_final: 0.8115 (m) REVERT: B 464 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8782 (ttmt) REVERT: B 479 TYR cc_start: 0.8261 (m-80) cc_final: 0.7925 (m-10) REVERT: B 489 ASP cc_start: 0.9122 (m-30) cc_final: 0.8787 (t0) REVERT: B 490 TRP cc_start: 0.8121 (t-100) cc_final: 0.7698 (t-100) REVERT: B 503 TYR cc_start: 0.8266 (t80) cc_final: 0.7858 (t80) REVERT: C 474 LYS cc_start: 0.9065 (mttm) cc_final: 0.8854 (mttt) REVERT: C 479 TYR cc_start: 0.8061 (m-80) cc_final: 0.7434 (m-80) REVERT: C 521 GLN cc_start: 0.8161 (pp30) cc_final: 0.7842 (pp30) REVERT: C 525 GLU cc_start: 0.8862 (mp0) cc_final: 0.8541 (mp0) REVERT: C 537 ARG cc_start: 0.8429 (tpp80) cc_final: 0.7967 (mtp-110) REVERT: D 414 GLU cc_start: 0.9207 (mp0) cc_final: 0.8709 (mp0) REVERT: D 431 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 454 ASP cc_start: 0.7553 (t0) cc_final: 0.7240 (t0) REVERT: D 472 GLU cc_start: 0.8433 (tp30) cc_final: 0.7775 (tp30) REVERT: D 476 PHE cc_start: 0.8672 (m-80) cc_final: 0.7777 (m-10) REVERT: D 478 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7333 (t0) REVERT: D 497 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8100 (ptp-170) REVERT: D 517 ARG cc_start: 0.9305 (mmm-85) cc_final: 0.9058 (mmm160) REVERT: D 522 GLN cc_start: 0.8520 (mt0) cc_final: 0.8192 (mm-40) REVERT: E 418 GLN cc_start: 0.8991 (mm110) cc_final: 0.8788 (mm110) REVERT: E 435 GLU cc_start: 0.9556 (tm-30) cc_final: 0.9303 (pp20) REVERT: E 543 ARG cc_start: 0.8834 (mmt90) cc_final: 0.8046 (mtm110) REVERT: F 426 PHE cc_start: 0.6320 (m-80) cc_final: 0.6015 (m-10) REVERT: F 429 TYR cc_start: 0.8146 (m-10) cc_final: 0.7897 (m-10) REVERT: F 457 MET cc_start: 0.6858 (mtt) cc_final: 0.6499 (mtp) REVERT: F 479 TYR cc_start: 0.7971 (m-80) cc_final: 0.7587 (m-80) REVERT: F 524 LEU cc_start: 0.8138 (tt) cc_final: 0.7668 (pp) REVERT: G 468 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8059 (ttp80) REVERT: G 503 TYR cc_start: 0.8724 (t80) cc_final: 0.8407 (t80) REVERT: G 522 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7445 (mm-40) REVERT: G 543 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8193 (mtm110) REVERT: H 418 GLN cc_start: 0.8724 (mm110) cc_final: 0.8423 (mm110) REVERT: H 430 CYS cc_start: 0.8611 (t) cc_final: 0.8384 (m) REVERT: H 476 PHE cc_start: 0.8993 (m-10) cc_final: 0.8793 (m-10) REVERT: H 486 ASN cc_start: 0.9328 (t0) cc_final: 0.8978 (t0) REVERT: H 545 MET cc_start: 0.5634 (ptt) cc_final: 0.5167 (ptt) outliers start: 30 outliers final: 21 residues processed: 391 average time/residue: 0.1147 time to fit residues: 59.4680 Evaluate side-chains 366 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 342 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.129359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.089887 restraints weight = 159317.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.097325 restraints weight = 40151.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.102781 restraints weight = 20429.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106638 restraints weight = 12811.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109487 restraints weight = 9017.549| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10140 Z= 0.179 Angle : 0.832 16.959 13664 Z= 0.417 Chirality : 0.047 0.213 1484 Planarity : 0.005 0.044 1767 Dihedral : 8.842 179.707 1460 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.11 % Allowed : 28.77 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1201 helix: 0.01 (0.19), residues: 771 sheet: None (None), residues: 0 loop : 0.65 (0.34), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 484 TYR 0.018 0.002 TYR E 429 PHE 0.021 0.001 PHE B 476 TRP 0.013 0.001 TRP D 490 HIS 0.004 0.001 HIS E 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (10132) covalent geometry : angle 0.83209 / 0.42 (13664) hydrogen bonds : bond 0.04707 / 3.02 ( 485) hydrogen bonds : angle 5.18258 / 3.70 ( 1327) Misc. bond : bond 0.00073 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 362 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6325 (mm) REVERT: A 411 SER cc_start: 0.8091 (m) cc_final: 0.7798 (t) REVERT: A 416 GLU cc_start: 0.9255 (mp0) cc_final: 0.9019 (mp0) REVERT: A 450 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8732 (pt0) REVERT: A 454 ASP cc_start: 0.7548 (m-30) cc_final: 0.7325 (t0) REVERT: A 472 GLU cc_start: 0.8351 (tp30) cc_final: 0.7943 (tp30) REVERT: A 476 PHE cc_start: 0.8526 (m-10) cc_final: 0.8306 (m-10) REVERT: A 478 ASN cc_start: 0.8725 (t0) cc_final: 0.8319 (t0) REVERT: A 503 TYR cc_start: 0.8742 (t80) cc_final: 0.8363 (t80) REVERT: A 522 GLN cc_start: 0.8482 (mm-40) cc_final: 0.7575 (mm-40) REVERT: A 529 ILE cc_start: 0.8337 (mt) cc_final: 0.7934 (tt) REVERT: A 530 HIS cc_start: 0.8679 (m90) cc_final: 0.8246 (m-70) REVERT: B 413 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8568 (tmtt) REVERT: B 435 GLU cc_start: 0.9557 (tm-30) cc_final: 0.8989 (pp20) REVERT: B 479 TYR cc_start: 0.8323 (m-80) cc_final: 0.8025 (m-10) REVERT: B 489 ASP cc_start: 0.9158 (m-30) cc_final: 0.8824 (t0) REVERT: B 490 TRP cc_start: 0.8146 (t-100) cc_final: 0.7738 (t-100) REVERT: C 479 TYR cc_start: 0.8348 (m-80) cc_final: 0.7733 (m-80) REVERT: C 520 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7920 (tm-30) REVERT: C 525 GLU cc_start: 0.8892 (mp0) cc_final: 0.8384 (mp0) REVERT: D 431 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8055 (tm-30) REVERT: D 472 GLU cc_start: 0.8407 (tp30) cc_final: 0.8021 (tp30) REVERT: D 476 PHE cc_start: 0.8735 (m-80) cc_final: 0.8171 (m-10) REVERT: D 478 ASN cc_start: 0.7812 (t0) cc_final: 0.7551 (t0) REVERT: D 497 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8144 (ptp-170) REVERT: D 522 GLN cc_start: 0.8685 (mt0) cc_final: 0.8346 (mm-40) REVERT: E 413 LYS cc_start: 0.9032 (tppp) cc_final: 0.8577 (tppp) REVERT: E 435 GLU cc_start: 0.9597 (tm-30) cc_final: 0.9300 (pp20) REVERT: F 426 PHE cc_start: 0.6467 (m-80) cc_final: 0.6174 (m-10) REVERT: F 479 TYR cc_start: 0.8111 (m-80) cc_final: 0.7676 (m-80) REVERT: G 423 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9056 (tm-30) REVERT: G 424 ILE cc_start: 0.8953 (pt) cc_final: 0.8644 (pt) REVERT: G 468 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8160 (ttp80) REVERT: G 497 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8404 (ptp90) REVERT: G 503 TYR cc_start: 0.8722 (t80) cc_final: 0.8437 (t80) REVERT: G 522 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7585 (mm-40) REVERT: H 418 GLN cc_start: 0.8791 (mm110) cc_final: 0.8528 (mm110) REVERT: H 486 ASN cc_start: 0.9357 (t0) cc_final: 0.8982 (t0) REVERT: H 522 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8030 (mm-40) REVERT: H 530 HIS cc_start: 0.8474 (m90) cc_final: 0.8204 (m-70) REVERT: H 545 MET cc_start: 0.5786 (ptt) cc_final: 0.5379 (ptt) outliers start: 34 outliers final: 25 residues processed: 383 average time/residue: 0.1115 time to fit residues: 57.9494 Evaluate side-chains 377 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 350 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 GLN A 452 GLN B 422 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS F 534 HIS G 436 GLN H 452 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.130445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.090672 restraints weight = 148036.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.098131 restraints weight = 39747.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.103588 restraints weight = 20612.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.107477 restraints weight = 13021.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.110370 restraints weight = 9197.960| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10140 Z= 0.166 Angle : 0.837 13.790 13664 Z= 0.417 Chirality : 0.045 0.209 1484 Planarity : 0.004 0.045 1767 Dihedral : 8.738 179.915 1460 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.11 % Allowed : 29.95 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1201 helix: -0.00 (0.19), residues: 771 sheet: None (None), residues: 0 loop : 0.56 (0.34), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 484 TYR 0.017 0.002 TYR F 429 PHE 0.022 0.001 PHE B 476 TRP 0.019 0.002 TRP D 490 HIS 0.008 0.001 HIS F 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (10132) covalent geometry : angle 0.83733 / 0.42 (13664) hydrogen bonds : bond 0.04464 / 2.86 ( 485) hydrogen bonds : angle 5.21226 / 3.72 ( 1327) Misc. bond : bond 0.00066 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 387 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.8074 (m) cc_final: 0.7804 (t) REVERT: A 450 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8591 (pt0) REVERT: A 469 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8630 (mm-30) REVERT: A 472 GLU cc_start: 0.8269 (tp30) cc_final: 0.7802 (tp30) REVERT: A 476 PHE cc_start: 0.8523 (m-10) cc_final: 0.8253 (m-10) REVERT: A 478 ASN cc_start: 0.8678 (t0) cc_final: 0.8299 (t0) REVERT: A 497 ARG cc_start: 0.8620 (mtm180) cc_final: 0.8247 (ptp90) REVERT: A 503 TYR cc_start: 0.8675 (t80) cc_final: 0.8345 (t80) REVERT: A 522 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7580 (mm-40) REVERT: A 525 GLU cc_start: 0.9086 (mp0) cc_final: 0.8785 (mp0) REVERT: A 530 HIS cc_start: 0.8685 (m90) cc_final: 0.8252 (m-70) REVERT: B 435 GLU cc_start: 0.9531 (tm-30) cc_final: 0.9131 (pp20) REVERT: B 479 TYR cc_start: 0.8365 (m-80) cc_final: 0.8139 (m-10) REVERT: B 489 ASP cc_start: 0.9099 (m-30) cc_final: 0.8797 (t0) REVERT: B 490 TRP cc_start: 0.8187 (t-100) cc_final: 0.7791 (t-100) REVERT: B 503 TYR cc_start: 0.8174 (t80) cc_final: 0.7734 (t80) REVERT: C 474 LYS cc_start: 0.9185 (mttt) cc_final: 0.8975 (mttp) REVERT: C 479 TYR cc_start: 0.8183 (m-80) cc_final: 0.7616 (m-80) REVERT: C 497 ARG cc_start: 0.9156 (mtm110) cc_final: 0.8434 (ptp90) REVERT: C 521 GLN cc_start: 0.8248 (pp30) cc_final: 0.7880 (pp30) REVERT: C 525 GLU cc_start: 0.8919 (mp0) cc_final: 0.8380 (mp0) REVERT: D 413 LYS cc_start: 0.9191 (tmtt) cc_final: 0.8905 (mmmm) REVERT: D 414 GLU cc_start: 0.9308 (mp0) cc_final: 0.8063 (mp0) REVERT: D 431 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 449 GLU cc_start: 0.8727 (pp20) cc_final: 0.8526 (pp20) REVERT: D 472 GLU cc_start: 0.8413 (tp30) cc_final: 0.8087 (tp30) REVERT: D 476 PHE cc_start: 0.8750 (m-80) cc_final: 0.8248 (m-10) REVERT: D 478 ASN cc_start: 0.7974 (t0) cc_final: 0.7650 (t0) REVERT: D 522 GLN cc_start: 0.8615 (mt0) cc_final: 0.8411 (mt0) REVERT: D 525 GLU cc_start: 0.9137 (mp0) cc_final: 0.8740 (mp0) REVERT: E 413 LYS cc_start: 0.9033 (tppp) cc_final: 0.8567 (tppp) REVERT: E 435 GLU cc_start: 0.9585 (tm-30) cc_final: 0.9276 (pp20) REVERT: F 414 GLU cc_start: 0.9305 (mp0) cc_final: 0.8716 (mm-30) REVERT: F 479 TYR cc_start: 0.8071 (m-80) cc_final: 0.7600 (m-80) REVERT: F 524 LEU cc_start: 0.8270 (tt) cc_final: 0.7837 (pp) REVERT: G 423 GLN cc_start: 0.9346 (tm-30) cc_final: 0.9087 (tm-30) REVERT: G 424 ILE cc_start: 0.8944 (pt) cc_final: 0.8671 (pt) REVERT: G 468 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8214 (ttp80) REVERT: G 497 ARG cc_start: 0.8865 (mtm-85) cc_final: 0.8407 (ptp90) REVERT: G 522 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7535 (mm-40) REVERT: G 543 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8149 (mtm110) REVERT: G 545 MET cc_start: 0.6496 (ptt) cc_final: 0.6243 (mmm) REVERT: H 486 ASN cc_start: 0.9325 (t0) cc_final: 0.8919 (t0) REVERT: H 530 HIS cc_start: 0.8482 (m90) cc_final: 0.8180 (m-70) REVERT: H 545 MET cc_start: 0.5840 (ptt) cc_final: 0.5414 (ptt) outliers start: 34 outliers final: 25 residues processed: 406 average time/residue: 0.1117 time to fit residues: 60.8604 Evaluate side-chains 389 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 363 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 518 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.128797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089318 restraints weight = 168279.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096776 restraints weight = 41591.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.102161 restraints weight = 21218.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.106008 restraints weight = 13304.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.108851 restraints weight = 9350.949| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10140 Z= 0.173 Angle : 0.875 12.162 13664 Z= 0.434 Chirality : 0.046 0.194 1484 Planarity : 0.005 0.052 1767 Dihedral : 8.669 179.750 1458 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.93 % Allowed : 30.05 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1201 helix: -0.12 (0.19), residues: 767 sheet: None (None), residues: 0 loop : 0.41 (0.34), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 484 TYR 0.019 0.002 TYR E 501 PHE 0.012 0.001 PHE H 476 TRP 0.016 0.002 TRP A 420 HIS 0.017 0.001 HIS F 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (10132) covalent geometry : angle 0.87490 / 0.43 (13664) hydrogen bonds : bond 0.04324 / 2.76 ( 485) hydrogen bonds : angle 5.29662 / 3.77 ( 1327) Misc. bond : bond 0.00058 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 370 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.8015 (m) cc_final: 0.7753 (t) REVERT: A 450 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8977 (pt0) REVERT: A 476 PHE cc_start: 0.8547 (m-10) cc_final: 0.8269 (m-10) REVERT: A 478 ASN cc_start: 0.8716 (t0) cc_final: 0.8359 (t0) REVERT: A 497 ARG cc_start: 0.8710 (mtm180) cc_final: 0.8350 (ptp90) REVERT: A 503 TYR cc_start: 0.8702 (t80) cc_final: 0.8307 (t80) REVERT: A 522 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7565 (mm-40) REVERT: A 530 HIS cc_start: 0.8639 (m90) cc_final: 0.8177 (m-70) REVERT: B 479 TYR cc_start: 0.8337 (m-80) cc_final: 0.8135 (m-10) REVERT: B 489 ASP cc_start: 0.9096 (m-30) cc_final: 0.8765 (t0) REVERT: B 490 TRP cc_start: 0.8178 (t-100) cc_final: 0.7787 (t-100) REVERT: B 503 TYR cc_start: 0.8221 (t80) cc_final: 0.7741 (t80) REVERT: C 474 LYS cc_start: 0.9240 (mttt) cc_final: 0.9037 (mttp) REVERT: C 479 TYR cc_start: 0.8175 (m-80) cc_final: 0.7691 (m-80) REVERT: C 497 ARG cc_start: 0.9151 (mtm110) cc_final: 0.8434 (ptp90) REVERT: C 520 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7949 (tm-30) REVERT: C 521 GLN cc_start: 0.8309 (pp30) cc_final: 0.7789 (pp30) REVERT: C 522 GLN cc_start: 0.8933 (pt0) cc_final: 0.8589 (pm20) REVERT: C 525 GLU cc_start: 0.8903 (mp0) cc_final: 0.8393 (mp0) REVERT: D 413 LYS cc_start: 0.9172 (tmtt) cc_final: 0.8931 (mmmm) REVERT: D 414 GLU cc_start: 0.9330 (mp0) cc_final: 0.8141 (mp0) REVERT: D 431 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8064 (tm-30) REVERT: D 472 GLU cc_start: 0.8443 (tp30) cc_final: 0.8085 (tp30) REVERT: D 476 PHE cc_start: 0.8714 (m-80) cc_final: 0.8228 (m-10) REVERT: D 497 ARG cc_start: 0.8325 (ptp-110) cc_final: 0.8015 (ptp90) REVERT: D 520 GLU cc_start: 0.7648 (pm20) cc_final: 0.6186 (mm-30) REVERT: D 522 GLN cc_start: 0.8653 (mt0) cc_final: 0.8249 (mm-40) REVERT: D 525 GLU cc_start: 0.9155 (mp0) cc_final: 0.8751 (mp0) REVERT: E 413 LYS cc_start: 0.9048 (tppp) cc_final: 0.8592 (tppp) REVERT: E 435 GLU cc_start: 0.9576 (tm-30) cc_final: 0.9237 (pp20) REVERT: E 497 ARG cc_start: 0.9094 (mtm180) cc_final: 0.8624 (ptp90) REVERT: F 414 GLU cc_start: 0.9343 (mp0) cc_final: 0.9015 (mp0) REVERT: F 457 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7048 (mmm) REVERT: F 479 TYR cc_start: 0.8084 (m-80) cc_final: 0.7598 (m-80) REVERT: F 522 GLN cc_start: 0.8695 (mt0) cc_final: 0.8210 (mm-40) REVERT: F 524 LEU cc_start: 0.8279 (tt) cc_final: 0.7534 (pp) REVERT: G 414 GLU cc_start: 0.9378 (mp0) cc_final: 0.8882 (mp0) REVERT: G 423 GLN cc_start: 0.9350 (tm-30) cc_final: 0.9118 (tm-30) REVERT: G 424 ILE cc_start: 0.8889 (pt) cc_final: 0.8643 (pt) REVERT: G 479 TYR cc_start: 0.7871 (m-80) cc_final: 0.7652 (m-80) REVERT: G 497 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8398 (ptp90) REVERT: G 521 GLN cc_start: 0.9140 (tt0) cc_final: 0.8649 (pp30) REVERT: G 522 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8130 (mt0) REVERT: G 543 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8140 (mtm110) REVERT: H 413 LYS cc_start: 0.9151 (tppp) cc_final: 0.8682 (tmtt) REVERT: H 486 ASN cc_start: 0.9345 (t0) cc_final: 0.8930 (t0) REVERT: H 522 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8465 (mm-40) REVERT: H 530 HIS cc_start: 0.8487 (m90) cc_final: 0.8180 (m-70) REVERT: H 545 MET cc_start: 0.5862 (ptt) cc_final: 0.5380 (ptt) outliers start: 32 outliers final: 28 residues processed: 388 average time/residue: 0.1138 time to fit residues: 59.7711 Evaluate side-chains 388 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 359 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 518 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.128535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.089195 restraints weight = 168182.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096553 restraints weight = 41752.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.101957 restraints weight = 21339.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.105766 restraints weight = 13382.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.108645 restraints weight = 9395.386| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10140 Z= 0.178 Angle : 0.903 13.282 13664 Z= 0.445 Chirality : 0.046 0.224 1484 Planarity : 0.005 0.047 1767 Dihedral : 8.616 179.744 1458 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.20 % Allowed : 29.95 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1201 helix: -0.17 (0.19), residues: 766 sheet: None (None), residues: 0 loop : 0.41 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 484 TYR 0.021 0.002 TYR H 429 PHE 0.010 0.001 PHE G 476 TRP 0.016 0.002 TRP D 490 HIS 0.009 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (10132) covalent geometry : angle 0.90283 / 0.44 (13664) hydrogen bonds : bond 0.04308 / 2.77 ( 485) hydrogen bonds : angle 5.35827 / 3.80 ( 1327) Misc. bond : bond 0.00058 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.8008 (m) cc_final: 0.7756 (t) REVERT: A 450 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9017 (pt0) REVERT: A 472 GLU cc_start: 0.8352 (tp30) cc_final: 0.7932 (tp30) REVERT: A 478 ASN cc_start: 0.8765 (t0) cc_final: 0.8397 (t0) REVERT: A 497 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8402 (ptp90) REVERT: A 503 TYR cc_start: 0.8727 (t80) cc_final: 0.8376 (t80) REVERT: A 522 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7618 (mm-40) REVERT: A 525 GLU cc_start: 0.9089 (mp0) cc_final: 0.8668 (mp0) REVERT: A 530 HIS cc_start: 0.8685 (m90) cc_final: 0.8208 (m-70) REVERT: B 479 TYR cc_start: 0.8307 (m-80) cc_final: 0.8104 (m-10) REVERT: B 489 ASP cc_start: 0.9139 (m-30) cc_final: 0.8885 (t0) REVERT: B 490 TRP cc_start: 0.8177 (t-100) cc_final: 0.7781 (t-100) REVERT: B 503 TYR cc_start: 0.8256 (t80) cc_final: 0.7772 (t80) REVERT: B 521 GLN cc_start: 0.8462 (tp40) cc_final: 0.8176 (pp30) REVERT: B 522 GLN cc_start: 0.8701 (mt0) cc_final: 0.8376 (mm-40) REVERT: C 479 TYR cc_start: 0.8116 (m-80) cc_final: 0.7635 (m-80) REVERT: C 497 ARG cc_start: 0.9139 (mtm110) cc_final: 0.8423 (ptp90) REVERT: C 520 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 521 GLN cc_start: 0.8326 (pp30) cc_final: 0.7778 (pp30) REVERT: C 522 GLN cc_start: 0.8945 (pt0) cc_final: 0.8554 (pm20) REVERT: C 525 GLU cc_start: 0.8907 (mp0) cc_final: 0.8397 (mp0) REVERT: D 413 LYS cc_start: 0.9174 (tmtt) cc_final: 0.8950 (mmmm) REVERT: D 414 GLU cc_start: 0.9297 (mp0) cc_final: 0.8073 (mp0) REVERT: D 431 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 472 GLU cc_start: 0.8457 (tp30) cc_final: 0.8041 (tm-30) REVERT: D 476 PHE cc_start: 0.8697 (m-80) cc_final: 0.8417 (m-10) REVERT: D 497 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8097 (ptp90) REVERT: D 525 GLU cc_start: 0.9156 (mp0) cc_final: 0.8749 (mp0) REVERT: E 413 LYS cc_start: 0.9040 (tppp) cc_final: 0.8576 (tppp) REVERT: E 497 ARG cc_start: 0.9095 (mtm180) cc_final: 0.8651 (ptp90) REVERT: F 414 GLU cc_start: 0.9325 (mp0) cc_final: 0.8613 (mm-30) REVERT: F 457 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6989 (mmm) REVERT: F 479 TYR cc_start: 0.8106 (m-80) cc_final: 0.7683 (m-80) REVERT: F 522 GLN cc_start: 0.8713 (mt0) cc_final: 0.8234 (mm-40) REVERT: F 524 LEU cc_start: 0.8272 (tt) cc_final: 0.7528 (pp) REVERT: G 414 GLU cc_start: 0.9399 (mp0) cc_final: 0.8906 (mp0) REVERT: G 423 GLN cc_start: 0.9340 (tm-30) cc_final: 0.9121 (tm-30) REVERT: G 424 ILE cc_start: 0.8924 (pt) cc_final: 0.8682 (pt) REVERT: G 431 GLU cc_start: 0.8766 (tp30) cc_final: 0.8513 (tm-30) REVERT: G 479 TYR cc_start: 0.7867 (m-80) cc_final: 0.7664 (m-80) REVERT: G 497 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8438 (ptp90) REVERT: G 521 GLN cc_start: 0.9208 (tt0) cc_final: 0.8725 (pp30) REVERT: G 522 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8162 (mt0) REVERT: H 413 LYS cc_start: 0.9155 (tppp) cc_final: 0.8665 (tmtt) REVERT: H 454 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7399 (t0) REVERT: H 486 ASN cc_start: 0.9350 (t0) cc_final: 0.8974 (t0) REVERT: H 522 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8449 (mm-40) REVERT: H 525 GLU cc_start: 0.8951 (mp0) cc_final: 0.8699 (mp0) REVERT: H 530 HIS cc_start: 0.8438 (m90) cc_final: 0.8071 (m-70) REVERT: H 545 MET cc_start: 0.5956 (ptt) cc_final: 0.5560 (ptt) outliers start: 35 outliers final: 28 residues processed: 386 average time/residue: 0.1116 time to fit residues: 58.2273 Evaluate side-chains 386 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 356 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 518 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 48 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.128105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.088844 restraints weight = 158043.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.096123 restraints weight = 41598.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101403 restraints weight = 21578.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.105201 restraints weight = 13647.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.107986 restraints weight = 9647.973| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10140 Z= 0.174 Angle : 0.918 12.611 13664 Z= 0.452 Chirality : 0.047 0.245 1484 Planarity : 0.005 0.058 1767 Dihedral : 8.579 179.824 1456 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.65 % Allowed : 30.68 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1201 helix: -0.19 (0.19), residues: 766 sheet: None (None), residues: 0 loop : 0.41 (0.35), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 517 TYR 0.017 0.002 TYR H 479 PHE 0.014 0.001 PHE B 476 TRP 0.014 0.002 TRP C 490 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (10132) covalent geometry : angle 0.91827 / 0.45 (13664) hydrogen bonds : bond 0.04226 / 2.71 ( 485) hydrogen bonds : angle 5.41687 / 3.85 ( 1327) Misc. bond : bond 0.00054 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 369 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7994 (m) cc_final: 0.7677 (t) REVERT: A 416 GLU cc_start: 0.9291 (mp0) cc_final: 0.8992 (mp0) REVERT: A 444 LEU cc_start: 0.8622 (mp) cc_final: 0.8403 (mt) REVERT: A 450 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8745 (pt0) REVERT: A 472 GLU cc_start: 0.8350 (tp30) cc_final: 0.8070 (tp30) REVERT: A 478 ASN cc_start: 0.8721 (t0) cc_final: 0.8376 (t0) REVERT: A 497 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8439 (ptp90) REVERT: A 503 TYR cc_start: 0.8754 (t80) cc_final: 0.8420 (t80) REVERT: A 522 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7598 (mm-40) REVERT: A 530 HIS cc_start: 0.8654 (m90) cc_final: 0.8150 (m-70) REVERT: B 489 ASP cc_start: 0.9144 (m-30) cc_final: 0.8882 (t0) REVERT: B 490 TRP cc_start: 0.8164 (t-100) cc_final: 0.7773 (t-100) REVERT: B 503 TYR cc_start: 0.8326 (t80) cc_final: 0.7859 (t80) REVERT: B 521 GLN cc_start: 0.8437 (tp40) cc_final: 0.8225 (pp30) REVERT: C 479 TYR cc_start: 0.8153 (m-80) cc_final: 0.7672 (m-80) REVERT: C 520 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 521 GLN cc_start: 0.8340 (pp30) cc_final: 0.7414 (pp30) REVERT: C 522 GLN cc_start: 0.8955 (pt0) cc_final: 0.8581 (pm20) REVERT: C 525 GLU cc_start: 0.8886 (mp0) cc_final: 0.8233 (mp0) REVERT: D 431 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8024 (tm-30) REVERT: D 469 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8794 (mm-30) REVERT: D 472 GLU cc_start: 0.8455 (tp30) cc_final: 0.8002 (tm-30) REVERT: D 476 PHE cc_start: 0.8688 (m-80) cc_final: 0.8409 (m-10) REVERT: D 520 GLU cc_start: 0.8010 (pm20) cc_final: 0.6663 (mm-30) REVERT: D 525 GLU cc_start: 0.9111 (mp0) cc_final: 0.8685 (mp0) REVERT: D 526 ASP cc_start: 0.7275 (m-30) cc_final: 0.7021 (m-30) REVERT: E 413 LYS cc_start: 0.9056 (tppp) cc_final: 0.8590 (tppp) REVERT: E 414 GLU cc_start: 0.9063 (pm20) cc_final: 0.8590 (pm20) REVERT: E 431 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8593 (tm-30) REVERT: E 435 GLU cc_start: 0.9573 (tm-30) cc_final: 0.9207 (pp20) REVERT: E 497 ARG cc_start: 0.9128 (mtm180) cc_final: 0.8702 (ptp90) REVERT: E 543 ARG cc_start: 0.9007 (mmt90) cc_final: 0.8225 (mtm110) REVERT: F 414 GLU cc_start: 0.9343 (mp0) cc_final: 0.8989 (mp0) REVERT: F 451 LEU cc_start: 0.9206 (tp) cc_final: 0.8905 (tp) REVERT: F 457 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6173 (mmp) REVERT: F 479 TYR cc_start: 0.8115 (m-80) cc_final: 0.7692 (m-80) REVERT: F 522 GLN cc_start: 0.8731 (mt0) cc_final: 0.8263 (mm-40) REVERT: F 524 LEU cc_start: 0.8314 (tt) cc_final: 0.7581 (pp) REVERT: G 414 GLU cc_start: 0.9411 (mp0) cc_final: 0.8967 (mp0) REVERT: G 423 GLN cc_start: 0.9356 (tm-30) cc_final: 0.9146 (tm-30) REVERT: G 424 ILE cc_start: 0.8927 (pt) cc_final: 0.8694 (pt) REVERT: G 497 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8393 (ptp90) REVERT: G 521 GLN cc_start: 0.9199 (tt0) cc_final: 0.8713 (pp30) REVERT: G 522 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8200 (mt0) REVERT: H 418 GLN cc_start: 0.8714 (mm110) cc_final: 0.8506 (mm110) REVERT: H 449 GLU cc_start: 0.9150 (tp30) cc_final: 0.8946 (tp30) REVERT: H 451 LEU cc_start: 0.9105 (tp) cc_final: 0.8884 (tp) REVERT: H 454 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7437 (t0) REVERT: H 486 ASN cc_start: 0.9345 (t0) cc_final: 0.8982 (t0) REVERT: H 522 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8430 (mm-40) REVERT: H 530 HIS cc_start: 0.8442 (m90) cc_final: 0.8083 (m-70) REVERT: H 545 MET cc_start: 0.6083 (ptt) cc_final: 0.5879 (ptt) outliers start: 29 outliers final: 26 residues processed: 380 average time/residue: 0.1084 time to fit residues: 56.2658 Evaluate side-chains 383 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 355 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 495 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 0.0020 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 44 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.130003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.090359 restraints weight = 165893.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.097680 restraints weight = 41757.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.103108 restraints weight = 21527.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.106960 restraints weight = 13554.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.109846 restraints weight = 9554.278| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.7388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10140 Z= 0.175 Angle : 0.932 14.167 13664 Z= 0.455 Chirality : 0.046 0.228 1484 Planarity : 0.004 0.054 1767 Dihedral : 8.547 179.995 1456 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.01 % Allowed : 32.15 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1201 helix: -0.23 (0.19), residues: 763 sheet: None (None), residues: 0 loop : 0.36 (0.34), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 484 TYR 0.021 0.002 TYR E 503 PHE 0.017 0.001 PHE A 476 TRP 0.017 0.001 TRP C 490 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (10132) covalent geometry : angle 0.93158 / 0.45 (13664) hydrogen bonds : bond 0.04084 / 2.64 ( 485) hydrogen bonds : angle 5.40352 / 3.83 ( 1327) Misc. bond : bond 0.00046 / 0.02 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 370 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7982 (m) cc_final: 0.7737 (t) REVERT: A 444 LEU cc_start: 0.8612 (mp) cc_final: 0.8320 (mp) REVERT: A 450 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8827 (pt0) REVERT: A 478 ASN cc_start: 0.8682 (t0) cc_final: 0.8356 (t0) REVERT: A 479 TYR cc_start: 0.8357 (m-80) cc_final: 0.8143 (m-80) REVERT: A 487 LEU cc_start: 0.8851 (mt) cc_final: 0.8645 (mt) REVERT: A 497 ARG cc_start: 0.8764 (mtm180) cc_final: 0.8441 (ptp90) REVERT: A 503 TYR cc_start: 0.8705 (t80) cc_final: 0.8443 (t80) REVERT: A 525 GLU cc_start: 0.9032 (mp0) cc_final: 0.8644 (mp0) REVERT: A 530 HIS cc_start: 0.8688 (m90) cc_final: 0.8166 (m-70) REVERT: B 489 ASP cc_start: 0.9148 (m-30) cc_final: 0.8827 (t0) REVERT: B 490 TRP cc_start: 0.8136 (t-100) cc_final: 0.7796 (t-100) REVERT: B 503 TYR cc_start: 0.8319 (t80) cc_final: 0.7867 (t80) REVERT: C 479 TYR cc_start: 0.8064 (m-80) cc_final: 0.7619 (m-80) REVERT: C 497 ARG cc_start: 0.9125 (mtm110) cc_final: 0.8421 (ptp90) REVERT: C 520 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 521 GLN cc_start: 0.8333 (pp30) cc_final: 0.7705 (pp30) REVERT: C 522 GLN cc_start: 0.8874 (pt0) cc_final: 0.8614 (pm20) REVERT: C 523 LEU cc_start: 0.9023 (tp) cc_final: 0.8780 (tp) REVERT: C 525 GLU cc_start: 0.8834 (mp0) cc_final: 0.8272 (mp0) REVERT: D 411 SER cc_start: 0.8042 (m) cc_final: 0.7722 (t) REVERT: D 414 GLU cc_start: 0.9061 (mp0) cc_final: 0.8226 (mp0) REVERT: D 431 GLU cc_start: 0.8584 (tm-30) cc_final: 0.7975 (tm-30) REVERT: D 472 GLU cc_start: 0.8458 (tp30) cc_final: 0.8020 (tm-30) REVERT: D 476 PHE cc_start: 0.8685 (m-80) cc_final: 0.8423 (m-10) REVERT: D 520 GLU cc_start: 0.7821 (pm20) cc_final: 0.6578 (mm-30) REVERT: D 525 GLU cc_start: 0.9086 (mp0) cc_final: 0.8711 (mp0) REVERT: E 413 LYS cc_start: 0.9027 (tppp) cc_final: 0.8569 (tppp) REVERT: E 497 ARG cc_start: 0.9112 (mtm180) cc_final: 0.8742 (ptp90) REVERT: F 414 GLU cc_start: 0.9350 (mp0) cc_final: 0.8982 (mp0) REVERT: F 416 GLU cc_start: 0.8763 (mp0) cc_final: 0.8448 (pm20) REVERT: F 451 LEU cc_start: 0.9200 (tp) cc_final: 0.8899 (tp) REVERT: F 457 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6167 (mmp) REVERT: F 479 TYR cc_start: 0.7995 (m-80) cc_final: 0.7605 (m-80) REVERT: F 522 GLN cc_start: 0.8711 (mt0) cc_final: 0.8243 (mm-40) REVERT: F 524 LEU cc_start: 0.8280 (tt) cc_final: 0.7675 (pp) REVERT: G 414 GLU cc_start: 0.9418 (mp0) cc_final: 0.8991 (mp0) REVERT: G 424 ILE cc_start: 0.8898 (pt) cc_final: 0.8671 (pt) REVERT: G 431 GLU cc_start: 0.8805 (tp30) cc_final: 0.8531 (tm-30) REVERT: G 450 GLU cc_start: 0.9244 (mp0) cc_final: 0.8955 (pm20) REVERT: G 497 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8355 (ptp90) REVERT: G 521 GLN cc_start: 0.9126 (tt0) cc_final: 0.8578 (pp30) REVERT: H 418 GLN cc_start: 0.8657 (mm110) cc_final: 0.8431 (mm110) REVERT: H 449 GLU cc_start: 0.9086 (tp30) cc_final: 0.8877 (tp30) REVERT: H 486 ASN cc_start: 0.9312 (t0) cc_final: 0.8958 (t0) REVERT: H 501 TYR cc_start: 0.8352 (m-80) cc_final: 0.7955 (m-80) REVERT: H 522 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8391 (mm-40) REVERT: H 530 HIS cc_start: 0.8439 (m90) cc_final: 0.8019 (m-70) outliers start: 22 outliers final: 19 residues processed: 377 average time/residue: 0.1078 time to fit residues: 55.6820 Evaluate side-chains 377 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 357 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 452 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 10.0000 chunk 75 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN H 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.127465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090171 restraints weight = 157191.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097115 restraints weight = 39124.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.102205 restraints weight = 19995.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.105921 restraints weight = 12518.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.108563 restraints weight = 8739.174| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 97 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10140 Z= 0.179 Angle : 0.920 13.701 13664 Z= 0.451 Chirality : 0.047 0.223 1484 Planarity : 0.004 0.059 1767 Dihedral : 8.496 179.843 1456 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.11 % Allowed : 31.87 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1201 helix: -0.21 (0.19), residues: 764 sheet: None (None), residues: 0 loop : 0.45 (0.35), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 484 TYR 0.033 0.002 TYR E 503 PHE 0.016 0.001 PHE B 476 TRP 0.014 0.001 TRP C 490 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (10132) covalent geometry : angle 0.91961 / 0.45 (13664) hydrogen bonds : bond 0.04087 / 2.64 ( 485) hydrogen bonds : angle 5.39217 / 3.83 ( 1327) Misc. bond : bond 0.00056 / 0.03 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.21 seconds wall clock time: 43 minutes 9.07 seconds (2589.07 seconds total)