Starting phenix.real_space_refine on Sun Jul 27 22:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zg1_11191/07_2025/6zg1_11191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zg1_11191/07_2025/6zg1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zg1_11191/07_2025/6zg1_11191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zg1_11191/07_2025/6zg1_11191.map" model { file = "/net/cci-nas-00/data/ceres_data/6zg1_11191/07_2025/6zg1_11191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zg1_11191/07_2025/6zg1_11191.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.20, per 1000 atoms: 1.13 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: 2.70 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.21 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: 2.57 Time building geometry restraints manager: 3.06 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: 5974 35.95 - 71.90: 219 71.90 - 107.85: 35 107.85 - 143.80: 1 143.80 - 179.75: 2 Dihedral angle restraints: 6231 sinusoidal: 2661 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 6228 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.220 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 18.790 179.752 3943 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (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 TRP 0.034 0.008 TRP C 420 HIS 0.015 0.004 HIS E 534 PHE 0.046 0.009 PHE E 476 TYR 0.041 0.009 TYR D 429 ARG 0.020 0.002 ARG F 468 Details of bonding type rmsd hydrogen bonds : bond 0.19833 ( 485) hydrogen bonds : angle 6.68849 ( 1327) covalent geometry : bond 0.00958 (10132) covalent geometry : angle 1.60849 (13664) Misc. bond : bond 0.05001 ( 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 : 1.064 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: 0.4344 (mm) REVERT: A 411 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.6796 (t) REVERT: A 424 ILE cc_start: 0.7374 (pt) cc_final: 0.6991 (pt) REVERT: B 411 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6697 (t) REVERT: C 447 THR cc_start: 0.7912 (p) cc_final: 0.7700 (p) REVERT: D 424 ILE cc_start: 0.7058 (pt) cc_final: 0.6572 (pt) REVERT: D 473 LEU cc_start: 0.7961 (tp) cc_final: 0.7751 (tp) REVERT: D 476 PHE cc_start: 0.7518 (m-80) cc_final: 0.7314 (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: 0.8171 (p) cc_final: 0.7719 (p) REVERT: F 524 LEU cc_start: 0.7482 (tp) cc_final: 0.7228 (tt) REVERT: G 411 SER cc_start: 0.7975 (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: 0.8236 (tm-30) outliers start: 54 outliers final: 8 residues processed: 618 average time/residue: 0.3518 time to fit residues: 278.0634 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 : 1.247 ------------------------------------------------------------------------------- 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 95 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ** 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 452 GLN H 500 GLN H 530 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099352 restraints weight = 138354.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.108071 restraints weight = 37471.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.114431 restraints weight = 19100.597| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10140 Z= 0.188 Angle : 0.870 10.353 13664 Z= 0.447 Chirality : 0.045 0.159 1484 Planarity : 0.005 0.064 1767 Dihedral : 10.214 178.518 1481 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.11 % Allowed : 23.47 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1201 helix: -0.14 (0.18), residues: 770 sheet: None (None), residues: 0 loop : 0.95 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 490 HIS 0.010 0.002 HIS E 530 PHE 0.023 0.002 PHE B 476 TYR 0.030 0.003 TYR E 501 ARG 0.009 0.001 ARG D 517 Details of bonding type rmsd hydrogen bonds : bond 0.05855 ( 485) hydrogen bonds : angle 5.22606 ( 1327) covalent geometry : bond 0.00411 (10132) covalent geometry : angle 0.86965 (13664) Misc. bond : bond 0.00127 ( 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 458 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 424 time to evaluate : 1.742 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: A 405 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5803 (mm) REVERT: A 411 SER cc_start: 0.8235 (m) cc_final: 0.7815 (t) REVERT: A 414 GLU cc_start: 0.8878 (mp0) cc_final: 0.8547 (mp0) REVERT: A 416 GLU cc_start: 0.9385 (mp0) cc_final: 0.9106 (mp0) REVERT: A 476 PHE cc_start: 0.8937 (m-10) cc_final: 0.8715 (m-10) REVERT: A 503 TYR cc_start: 0.8705 (t80) cc_final: 0.8424 (t80) REVERT: A 525 GLU cc_start: 0.9042 (mp0) cc_final: 0.8816 (mp0) REVERT: B 435 GLU cc_start: 0.9565 (tm-30) cc_final: 0.9204 (pp20) REVERT: B 479 TYR cc_start: 0.8169 (m-80) cc_final: 0.7675 (m-10) REVERT: B 490 TRP cc_start: 0.8147 (t-100) cc_final: 0.7789 (t-100) REVERT: B 503 TYR cc_start: 0.8148 (t80) cc_final: 0.7857 (t80) REVERT: B 520 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 479 TYR cc_start: 0.7922 (m-80) cc_final: 0.7507 (m-80) REVERT: C 484 ARG cc_start: 0.9041 (ttm110) cc_final: 0.8766 (tmm160) REVERT: C 520 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 525 GLU cc_start: 0.8865 (mp0) cc_final: 0.8441 (mp0) REVERT: D 412 TRP cc_start: 0.7604 (m-10) cc_final: 0.7104 (m-10) REVERT: D 421 LEU cc_start: 0.8329 (mt) cc_final: 0.8066 (mt) REVERT: D 431 GLU cc_start: 0.8645 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 434 ARG cc_start: 0.8036 (tmm-80) cc_final: 0.7547 (tmm-80) REVERT: D 444 LEU cc_start: 0.8691 (mt) cc_final: 0.8470 (mt) REVERT: D 478 ASN cc_start: 0.7834 (t0) cc_final: 0.7620 (t0) REVERT: D 497 ARG cc_start: 0.8509 (mtm110) cc_final: 0.8200 (ptm160) REVERT: D 531 LEU cc_start: 0.6243 (tp) cc_final: 0.5991 (tp) REVERT: E 414 GLU cc_start: 0.8795 (mp0) cc_final: 0.8583 (mp0) REVERT: E 435 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9240 (pp20) REVERT: E 438 VAL cc_start: 0.8356 (t) cc_final: 0.8120 (m) REVERT: E 449 GLU cc_start: 0.8584 (tp30) cc_final: 0.8214 (tp30) REVERT: E 503 TYR cc_start: 0.8203 (t80) cc_final: 0.7958 (t80) REVERT: F 422 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8814 (mm-40) REVERT: F 473 LEU cc_start: 0.9370 (tp) cc_final: 0.9168 (mp) REVERT: F 476 PHE cc_start: 0.9139 (m-80) cc_final: 0.8797 (m-10) REVERT: F 479 TYR cc_start: 0.7801 (m-80) cc_final: 0.7445 (m-80) REVERT: F 531 LEU cc_start: 0.6945 (mt) cc_final: 0.6459 (tp) REVERT: G 414 GLU cc_start: 0.8409 (mp0) cc_final: 0.8134 (mm-30) REVERT: G 474 LYS cc_start: 0.9440 (mttt) cc_final: 0.9229 (mttp) REVERT: G 476 PHE cc_start: 0.9083 (m-80) cc_final: 0.8522 (m-10) REVERT: G 479 TYR cc_start: 0.8054 (m-80) cc_final: 0.7654 (m-80) REVERT: G 515 LEU cc_start: 0.9632 (tp) cc_final: 0.9409 (tp) REVERT: G 522 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7380 (mm-40) REVERT: G 543 ARG cc_start: 0.8833 (mtt180) cc_final: 0.8191 (mtm110) REVERT: G 545 MET cc_start: 0.7245 (ptp) cc_final: 0.6889 (ptt) REVERT: H 431 GLU cc_start: 0.9152 (tt0) cc_final: 0.8930 (tm-30) REVERT: H 438 VAL cc_start: 0.8188 (t) cc_final: 0.7964 (m) REVERT: H 476 PHE cc_start: 0.8885 (m-80) cc_final: 0.8633 (m-10) REVERT: H 545 MET cc_start: 0.5828 (ptt) cc_final: 0.5204 (ptt) outliers start: 34 outliers final: 19 residues processed: 443 average time/residue: 0.2995 time to fit residues: 173.9069 Evaluate side-chains 373 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 352 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 417 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 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 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 422 GLN Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 416 GLU Chi-restraints excluded: chain H residue 461 ILE 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 84 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** C 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN C 516 HIS ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS F 422 GLN F 530 HIS H 530 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.131864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.092101 restraints weight = 151959.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.099769 restraints weight = 39083.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.105388 restraints weight = 19875.371| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10140 Z= 0.196 Angle : 0.824 9.715 13664 Z= 0.418 Chirality : 0.046 0.168 1484 Planarity : 0.005 0.056 1767 Dihedral : 9.681 179.952 1467 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.11 % Allowed : 26.03 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1201 helix: -0.01 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 0.90 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 490 HIS 0.008 0.001 HIS B 516 PHE 0.023 0.002 PHE B 476 TYR 0.019 0.003 TYR A 429 ARG 0.008 0.001 ARG H 484 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 485) hydrogen bonds : angle 5.11888 ( 1327) covalent geometry : bond 0.00445 (10132) covalent geometry : angle 0.82449 (13664) Misc. bond : bond 0.00121 ( 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 418 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 373 time to evaluate : 1.202 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: 0.6332 (OUTLIER) cc_final: 0.5969 (mm) REVERT: A 411 SER cc_start: 0.8337 (m) cc_final: 0.8003 (t) REVERT: A 414 GLU cc_start: 0.8777 (mp0) cc_final: 0.8327 (mp0) REVERT: A 416 GLU cc_start: 0.9340 (mp0) cc_final: 0.9092 (mp0) REVERT: A 478 ASN cc_start: 0.8771 (t0) cc_final: 0.8521 (t0) REVERT: A 503 TYR cc_start: 0.8841 (t80) cc_final: 0.8507 (t80) REVERT: B 414 GLU cc_start: 0.9311 (mp0) cc_final: 0.9026 (pm20) REVERT: B 435 GLU cc_start: 0.9584 (tm-30) cc_final: 0.9232 (pp20) REVERT: B 438 VAL cc_start: 0.8442 (t) cc_final: 0.8056 (m) REVERT: B 449 GLU cc_start: 0.8551 (tp30) cc_final: 0.8295 (tp30) REVERT: B 450 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8626 (mt-10) REVERT: B 452 GLN cc_start: 0.8451 (pp30) cc_final: 0.8210 (tm-30) REVERT: B 479 TYR cc_start: 0.8254 (m-80) cc_final: 0.7796 (m-10) REVERT: B 489 ASP cc_start: 0.9202 (m-30) cc_final: 0.8875 (t0) REVERT: B 490 TRP cc_start: 0.8200 (t-100) cc_final: 0.7840 (t-100) REVERT: B 503 TYR cc_start: 0.8429 (t80) cc_final: 0.7960 (t80) REVERT: C 468 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6870 (mtm-85) REVERT: C 474 LYS cc_start: 0.9143 (mttm) cc_final: 0.8880 (mttt) REVERT: C 479 TYR cc_start: 0.8223 (m-80) cc_final: 0.7685 (m-80) REVERT: C 484 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8724 (tmm160) REVERT: C 490 TRP cc_start: 0.8647 (t-100) cc_final: 0.8205 (t-100) REVERT: C 521 GLN cc_start: 0.8255 (pp30) cc_final: 0.7829 (pp30) REVERT: C 525 GLU cc_start: 0.8776 (mp0) cc_final: 0.8262 (mp0) REVERT: D 414 GLU cc_start: 0.9180 (mp0) cc_final: 0.8767 (mp0) REVERT: D 421 LEU cc_start: 0.8440 (mt) cc_final: 0.8213 (mt) REVERT: D 431 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 449 GLU cc_start: 0.8806 (pp20) cc_final: 0.8481 (pp20) REVERT: D 472 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8302 (tp30) REVERT: D 476 PHE cc_start: 0.8853 (m-10) cc_final: 0.7791 (m-10) REVERT: D 497 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8198 (ptp-170) REVERT: D 545 MET cc_start: 0.4312 (ptm) cc_final: 0.4093 (ptm) REVERT: E 413 LYS cc_start: 0.9138 (tppp) cc_final: 0.8725 (tmtt) REVERT: E 435 GLU cc_start: 0.9576 (tm-30) cc_final: 0.9361 (pp20) REVERT: E 438 VAL cc_start: 0.8441 (t) cc_final: 0.8229 (m) REVERT: E 449 GLU cc_start: 0.8608 (tp30) cc_final: 0.8370 (tp30) REVERT: E 503 TYR cc_start: 0.8209 (t80) cc_final: 0.7942 (t80) REVERT: F 479 TYR cc_start: 0.8042 (m-80) cc_final: 0.7649 (m-80) REVERT: G 479 TYR cc_start: 0.7962 (m-80) cc_final: 0.7759 (m-80) REVERT: G 522 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7591 (mm-40) REVERT: G 543 ARG cc_start: 0.8850 (mtt180) cc_final: 0.8217 (mtm110) REVERT: H 413 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8497 (tptp) REVERT: H 418 GLN cc_start: 0.8909 (mm110) cc_final: 0.8462 (mm110) REVERT: H 431 GLU cc_start: 0.9223 (tt0) cc_final: 0.8985 (tm-30) REVERT: H 438 VAL cc_start: 0.8417 (t) cc_final: 0.8168 (m) REVERT: H 545 MET cc_start: 0.5836 (ptt) cc_final: 0.5344 (ptt) outliers start: 45 outliers final: 27 residues processed: 392 average time/residue: 0.2685 time to fit residues: 139.0063 Evaluate side-chains 373 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 344 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 474 LYS Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 ILE 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 447 THR 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 437 GLN 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 G residue 495 ASP Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 69 optimal weight: 0.0050 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 530 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.132612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.091283 restraints weight = 166373.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.099208 restraints weight = 41461.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.104937 restraints weight = 21091.545| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6072 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= 0.162 Angle : 0.836 14.352 13664 Z= 0.413 Chirality : 0.047 0.312 1484 Planarity : 0.005 0.060 1767 Dihedral : 9.247 179.965 1464 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.11 % Allowed : 27.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1201 helix: 0.09 (0.19), residues: 771 sheet: None (None), residues: 0 loop : 0.71 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 490 HIS 0.014 0.001 HIS E 530 PHE 0.017 0.001 PHE B 476 TYR 0.033 0.002 TYR F 429 ARG 0.008 0.001 ARG H 517 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 485) hydrogen bonds : angle 5.05713 ( 1327) covalent geometry : bond 0.00372 (10132) covalent geometry : angle 0.83621 (13664) Misc. bond : bond 0.00063 ( 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 411 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 377 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6489 (mm) REVERT: A 411 SER cc_start: 0.8281 (m) cc_final: 0.8033 (t) REVERT: A 414 GLU cc_start: 0.8734 (mp0) cc_final: 0.8155 (mp0) REVERT: A 444 LEU cc_start: 0.8793 (mt) cc_final: 0.8485 (mt) REVERT: A 450 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8684 (mt-10) REVERT: A 454 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6909 (t0) REVERT: A 476 PHE cc_start: 0.8407 (m-10) cc_final: 0.8162 (m-10) REVERT: A 478 ASN cc_start: 0.8770 (t0) cc_final: 0.8420 (t0) REVERT: A 503 TYR cc_start: 0.8788 (t80) cc_final: 0.8450 (t80) REVERT: B 413 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8706 (tmtt) REVERT: B 435 GLU cc_start: 0.9542 (tm-30) cc_final: 0.9205 (pp20) REVERT: B 438 VAL cc_start: 0.8393 (t) cc_final: 0.8192 (m) REVERT: B 449 GLU cc_start: 0.8657 (tp30) cc_final: 0.8340 (tp30) REVERT: B 452 GLN cc_start: 0.8500 (pp30) cc_final: 0.8217 (tm-30) REVERT: B 457 MET cc_start: 0.7210 (mtt) cc_final: 0.6467 (mtp) REVERT: B 464 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8830 (ttmt) REVERT: B 479 TYR cc_start: 0.8280 (m-80) cc_final: 0.7961 (m-10) REVERT: B 489 ASP cc_start: 0.9157 (m-30) cc_final: 0.8833 (t0) REVERT: B 490 TRP cc_start: 0.8122 (t-100) cc_final: 0.7711 (t-100) REVERT: B 517 ARG cc_start: 0.9146 (ttt-90) cc_final: 0.8939 (mtp85) REVERT: C 450 GLU cc_start: 0.9189 (mp0) cc_final: 0.8989 (pm20) REVERT: C 468 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7015 (mtm-85) REVERT: C 474 LYS cc_start: 0.9172 (mttm) cc_final: 0.8930 (mttt) REVERT: C 479 TYR cc_start: 0.8121 (m-80) cc_final: 0.7469 (m-80) REVERT: C 490 TRP cc_start: 0.8607 (t-100) cc_final: 0.8266 (t-100) REVERT: C 520 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 521 GLN cc_start: 0.8238 (pp30) cc_final: 0.7991 (pp30) REVERT: C 525 GLU cc_start: 0.8868 (mp0) cc_final: 0.8395 (mp0) REVERT: C 529 ILE cc_start: 0.8872 (mt) cc_final: 0.8598 (pt) REVERT: D 414 GLU cc_start: 0.9144 (mp0) cc_final: 0.8660 (mp0) REVERT: D 421 LEU cc_start: 0.8285 (mt) cc_final: 0.8026 (mt) REVERT: D 431 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 454 ASP cc_start: 0.7591 (t0) cc_final: 0.7286 (t0) REVERT: D 472 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8325 (tp30) REVERT: D 476 PHE cc_start: 0.8808 (m-10) cc_final: 0.7985 (m-10) REVERT: D 478 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7353 (t0) REVERT: D 497 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8115 (ptp-170) REVERT: D 517 ARG cc_start: 0.9351 (mmm-85) cc_final: 0.9067 (mmm160) REVERT: D 522 GLN cc_start: 0.8654 (mt0) cc_final: 0.8349 (mm-40) REVERT: E 435 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9319 (pp20) REVERT: E 438 VAL cc_start: 0.8468 (t) cc_final: 0.8226 (m) REVERT: E 449 GLU cc_start: 0.8539 (tp30) cc_final: 0.8314 (tp30) REVERT: E 543 ARG cc_start: 0.8807 (mmt90) cc_final: 0.8087 (mtm110) REVERT: F 429 TYR cc_start: 0.8554 (m-80) cc_final: 0.8281 (m-80) REVERT: F 479 TYR cc_start: 0.7947 (m-80) cc_final: 0.7495 (m-80) REVERT: G 479 TYR cc_start: 0.8014 (m-80) cc_final: 0.7793 (m-80) REVERT: G 522 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7523 (mm-40) REVERT: H 418 GLN cc_start: 0.8848 (mm110) cc_final: 0.8396 (mm110) REVERT: H 431 GLU cc_start: 0.9234 (tt0) cc_final: 0.8956 (tm-30) REVERT: H 438 VAL cc_start: 0.8526 (t) cc_final: 0.8243 (m) REVERT: H 476 PHE cc_start: 0.8998 (m-10) cc_final: 0.8796 (m-10) REVERT: H 522 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8326 (tp-100) REVERT: H 545 MET cc_start: 0.5448 (ptt) cc_final: 0.5044 (ptt) outliers start: 34 outliers final: 22 residues processed: 395 average time/residue: 0.2650 time to fit residues: 138.6445 Evaluate side-chains 360 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 334 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 452 GLN Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 470 LEU 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 468 ARG Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 538 ILE 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 417 VAL Chi-restraints excluded: chain E residue 467 PHE 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 495 ASP 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 518 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 9.9990 chunk 71 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN C 436 GLN ** 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** E 500 GLN E 530 HIS F 530 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.130717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.089933 restraints weight = 162131.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.097584 restraints weight = 41020.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103199 restraints weight = 21021.626| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10140 Z= 0.171 Angle : 0.834 17.843 13664 Z= 0.412 Chirality : 0.047 0.302 1484 Planarity : 0.005 0.044 1767 Dihedral : 9.065 179.818 1464 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.02 % Allowed : 27.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1201 helix: 0.04 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.73 (0.34), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 490 HIS 0.007 0.001 HIS F 530 PHE 0.025 0.001 PHE G 476 TYR 0.025 0.003 TYR E 429 ARG 0.010 0.001 ARG G 484 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 485) hydrogen bonds : angle 5.17236 ( 1327) covalent geometry : bond 0.00406 (10132) covalent geometry : angle 0.83395 (13664) Misc. bond : bond 0.00063 ( 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: 33 poor density : 363 time to evaluate : 1.185 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: A 405 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6822 (mm) REVERT: A 411 SER cc_start: 0.8269 (m) cc_final: 0.8016 (t) REVERT: A 414 GLU cc_start: 0.8712 (mp0) cc_final: 0.8269 (mp0) REVERT: A 444 LEU cc_start: 0.8732 (mt) cc_final: 0.8496 (mt) REVERT: A 454 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.7078 (t0) REVERT: A 476 PHE cc_start: 0.8411 (m-10) cc_final: 0.8166 (m-10) REVERT: A 478 ASN cc_start: 0.8750 (t0) cc_final: 0.8347 (t0) REVERT: A 503 TYR cc_start: 0.8779 (t80) cc_final: 0.8437 (t80) REVERT: A 529 ILE cc_start: 0.8411 (mt) cc_final: 0.8006 (tt) REVERT: B 438 VAL cc_start: 0.8456 (t) cc_final: 0.8251 (m) REVERT: B 449 GLU cc_start: 0.8752 (tp30) cc_final: 0.8400 (tp30) REVERT: B 452 GLN cc_start: 0.8741 (pp30) cc_final: 0.8406 (tm-30) REVERT: B 464 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8807 (ttmt) REVERT: B 479 TYR cc_start: 0.8338 (m-80) cc_final: 0.8018 (m-10) REVERT: B 490 TRP cc_start: 0.8151 (t-100) cc_final: 0.7780 (t-100) REVERT: B 517 ARG cc_start: 0.9255 (ttt-90) cc_final: 0.8967 (mtp85) REVERT: B 521 GLN cc_start: 0.8477 (mm110) cc_final: 0.7864 (pp30) REVERT: C 450 GLU cc_start: 0.9219 (mp0) cc_final: 0.9010 (pm20) REVERT: C 474 LYS cc_start: 0.9186 (mttm) cc_final: 0.8980 (mttt) REVERT: C 479 TYR cc_start: 0.8242 (m-80) cc_final: 0.7728 (m-80) REVERT: C 490 TRP cc_start: 0.8580 (t-100) cc_final: 0.8285 (t-100) REVERT: C 520 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 525 GLU cc_start: 0.8900 (mp0) cc_final: 0.8363 (mp0) REVERT: D 421 LEU cc_start: 0.8295 (mt) cc_final: 0.8052 (mt) REVERT: D 431 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 447 THR cc_start: 0.8227 (p) cc_final: 0.7610 (p) REVERT: D 449 GLU cc_start: 0.8828 (pp20) cc_final: 0.8317 (pp20) REVERT: D 454 ASP cc_start: 0.7674 (t0) cc_final: 0.7403 (t0) REVERT: D 472 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8364 (tm-30) REVERT: D 473 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8643 (mt) REVERT: D 476 PHE cc_start: 0.8828 (m-10) cc_final: 0.8358 (m-10) REVERT: D 478 ASN cc_start: 0.7697 (t0) cc_final: 0.7455 (t0) REVERT: D 522 GLN cc_start: 0.8719 (mt0) cc_final: 0.8400 (mm-40) REVERT: E 413 LYS cc_start: 0.9096 (tppp) cc_final: 0.8714 (tmtt) REVERT: E 438 VAL cc_start: 0.8525 (t) cc_final: 0.8304 (m) REVERT: E 474 LYS cc_start: 0.9153 (mttt) cc_final: 0.8870 (mttm) REVERT: F 479 TYR cc_start: 0.8055 (m-80) cc_final: 0.7595 (m-80) REVERT: G 468 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8124 (ttp80) REVERT: G 479 TYR cc_start: 0.8045 (m-80) cc_final: 0.7716 (m-80) REVERT: G 497 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8414 (ptp90) REVERT: G 511 ASP cc_start: 0.8963 (m-30) cc_final: 0.8754 (m-30) REVERT: G 522 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7592 (mm-40) REVERT: H 431 GLU cc_start: 0.9272 (tt0) cc_final: 0.8975 (tm-30) REVERT: H 438 VAL cc_start: 0.8565 (t) cc_final: 0.8312 (m) REVERT: H 473 LEU cc_start: 0.9281 (tp) cc_final: 0.9072 (tp) REVERT: H 486 ASN cc_start: 0.9366 (t0) cc_final: 0.9003 (t0) REVERT: H 545 MET cc_start: 0.5352 (ptt) cc_final: 0.5010 (ptt) outliers start: 33 outliers final: 24 residues processed: 381 average time/residue: 0.2570 time to fit residues: 130.5115 Evaluate side-chains 371 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 343 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 452 GLN Chi-restraints excluded: chain A residue 454 ASP 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 422 GLN Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 461 ILE 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 437 GLN 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 419 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL 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 60 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 82 optimal weight: 0.0770 chunk 76 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** C 522 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** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.131113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.091547 restraints weight = 150365.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099087 restraints weight = 39463.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.104497 restraints weight = 20312.900| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6580 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= 0.164 Angle : 0.853 13.901 13664 Z= 0.420 Chirality : 0.046 0.334 1484 Planarity : 0.004 0.039 1767 Dihedral : 8.920 179.872 1464 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.02 % Allowed : 29.04 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1201 helix: -0.01 (0.19), residues: 770 sheet: None (None), residues: 0 loop : 0.64 (0.34), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 490 HIS 0.018 0.001 HIS F 530 PHE 0.018 0.001 PHE H 476 TYR 0.020 0.002 TYR H 503 ARG 0.010 0.001 ARG G 484 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 485) hydrogen bonds : angle 5.20206 ( 1327) covalent geometry : bond 0.00387 (10132) covalent geometry : angle 0.85254 (13664) Misc. bond : bond 0.00049 ( 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 404 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 1.040 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: A 411 SER cc_start: 0.8225 (m) cc_final: 0.7960 (t) REVERT: A 454 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6921 (t0) REVERT: A 469 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8594 (mm-30) REVERT: A 476 PHE cc_start: 0.8433 (m-10) cc_final: 0.8144 (m-10) REVERT: A 478 ASN cc_start: 0.8661 (t0) cc_final: 0.8296 (t0) REVERT: A 503 TYR cc_start: 0.8704 (t80) cc_final: 0.8391 (t80) REVERT: A 530 HIS cc_start: 0.8715 (m90) cc_final: 0.8235 (m-70) REVERT: A 544 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8677 (mm-30) REVERT: B 438 VAL cc_start: 0.8455 (t) cc_final: 0.8253 (m) REVERT: B 452 GLN cc_start: 0.8775 (pp30) cc_final: 0.8419 (tm-30) REVERT: B 464 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8812 (ttmt) REVERT: B 479 TYR cc_start: 0.8366 (m-80) cc_final: 0.8119 (m-10) REVERT: B 489 ASP cc_start: 0.9149 (m-30) cc_final: 0.8832 (t0) REVERT: B 490 TRP cc_start: 0.8125 (t-100) cc_final: 0.7725 (t-100) REVERT: B 503 TYR cc_start: 0.8136 (t80) cc_final: 0.7673 (t80) REVERT: B 517 ARG cc_start: 0.9222 (ttt-90) cc_final: 0.8962 (mtp85) REVERT: B 521 GLN cc_start: 0.8596 (mm110) cc_final: 0.8195 (pp30) REVERT: C 474 LYS cc_start: 0.9161 (mttm) cc_final: 0.8959 (mttt) REVERT: C 479 TYR cc_start: 0.8211 (m-80) cc_final: 0.7691 (m-80) REVERT: C 490 TRP cc_start: 0.8546 (t-100) cc_final: 0.8190 (t-100) REVERT: C 525 GLU cc_start: 0.8913 (mp0) cc_final: 0.8353 (mp0) REVERT: D 413 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8836 (mmmm) REVERT: D 414 GLU cc_start: 0.9352 (mp0) cc_final: 0.8176 (mp0) REVERT: D 421 LEU cc_start: 0.8238 (mt) cc_final: 0.7995 (mt) REVERT: D 431 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8099 (tm-30) REVERT: D 469 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8707 (mm-30) REVERT: D 472 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8333 (tm-30) REVERT: D 473 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8720 (mt) REVERT: D 476 PHE cc_start: 0.8802 (m-10) cc_final: 0.8284 (m-10) REVERT: D 478 ASN cc_start: 0.7926 (t0) cc_final: 0.7680 (t0) REVERT: D 522 GLN cc_start: 0.8724 (mt0) cc_final: 0.8504 (mt0) REVERT: E 413 LYS cc_start: 0.9087 (tppp) cc_final: 0.8733 (tmtt) REVERT: E 438 VAL cc_start: 0.8528 (t) cc_final: 0.8282 (m) REVERT: E 474 LYS cc_start: 0.9166 (mttt) cc_final: 0.8879 (mttp) REVERT: F 479 TYR cc_start: 0.8055 (m-80) cc_final: 0.7583 (m-80) REVERT: F 522 GLN cc_start: 0.8721 (mt0) cc_final: 0.8203 (mm-40) REVERT: F 524 LEU cc_start: 0.8205 (tt) cc_final: 0.7704 (pp) REVERT: G 468 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8179 (ttp80) REVERT: G 479 TYR cc_start: 0.7960 (m-80) cc_final: 0.7582 (m-80) REVERT: G 497 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8381 (ptp90) REVERT: G 522 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7574 (mm-40) REVERT: H 431 GLU cc_start: 0.9277 (tt0) cc_final: 0.8985 (tm-30) REVERT: H 438 VAL cc_start: 0.8562 (t) cc_final: 0.8262 (m) REVERT: H 486 ASN cc_start: 0.9375 (t0) cc_final: 0.9174 (t0) REVERT: H 503 TYR cc_start: 0.8348 (t80) cc_final: 0.8037 (t80) REVERT: H 522 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8174 (tp-100) REVERT: H 545 MET cc_start: 0.5597 (ptt) cc_final: 0.5308 (ptt) outliers start: 33 outliers final: 23 residues processed: 387 average time/residue: 0.2503 time to fit residues: 129.1054 Evaluate side-chains 376 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 350 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 454 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 473 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 461 ILE 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 437 GLN 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 G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 441 ASP 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 60 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.0040 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN C 522 GLN ** 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** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 534 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.130970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091253 restraints weight = 157976.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.098705 restraints weight = 40301.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.104201 restraints weight = 20670.774| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10140 Z= 0.165 Angle : 0.872 12.284 13664 Z= 0.424 Chirality : 0.047 0.314 1484 Planarity : 0.005 0.049 1767 Dihedral : 8.725 179.902 1462 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.65 % Allowed : 30.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1201 helix: -0.02 (0.19), residues: 766 sheet: None (None), residues: 0 loop : 0.46 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 490 HIS 0.006 0.001 HIS B 534 PHE 0.016 0.001 PHE B 476 TYR 0.019 0.002 TYR E 501 ARG 0.011 0.001 ARG D 517 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 485) hydrogen bonds : angle 5.26124 ( 1327) covalent geometry : bond 0.00391 (10132) covalent geometry : angle 0.87152 (13664) Misc. bond : bond 0.00048 ( 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 391 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 362 time to evaluate : 1.104 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: A 411 SER cc_start: 0.8182 (m) cc_final: 0.7932 (t) REVERT: A 450 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8739 (pp20) REVERT: A 454 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7052 (t0) REVERT: A 472 GLU cc_start: 0.8144 (tp30) cc_final: 0.7664 (tp30) REVERT: A 476 PHE cc_start: 0.8365 (m-10) cc_final: 0.8087 (m-10) REVERT: A 478 ASN cc_start: 0.8650 (t0) cc_final: 0.8312 (t0) REVERT: A 503 TYR cc_start: 0.8788 (t80) cc_final: 0.8470 (t80) REVERT: A 525 GLU cc_start: 0.9076 (mp0) cc_final: 0.8704 (mp0) REVERT: A 530 HIS cc_start: 0.8761 (m90) cc_final: 0.8286 (m-70) REVERT: A 544 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8679 (mm-30) REVERT: B 452 GLN cc_start: 0.8801 (pp30) cc_final: 0.8489 (tm-30) REVERT: B 489 ASP cc_start: 0.9171 (m-30) cc_final: 0.8877 (t0) REVERT: B 490 TRP cc_start: 0.8141 (t-100) cc_final: 0.7766 (t-100) REVERT: B 503 TYR cc_start: 0.8207 (t80) cc_final: 0.7716 (t80) REVERT: B 517 ARG cc_start: 0.9270 (ttt-90) cc_final: 0.9031 (mtp85) REVERT: B 521 GLN cc_start: 0.8546 (mm110) cc_final: 0.8199 (pp30) REVERT: B 522 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8340 (tp-100) REVERT: C 479 TYR cc_start: 0.8167 (m-80) cc_final: 0.7613 (m-80) REVERT: C 490 TRP cc_start: 0.8497 (t-100) cc_final: 0.8177 (t-100) REVERT: C 520 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7945 (tm-30) REVERT: C 525 GLU cc_start: 0.8821 (mp0) cc_final: 0.8281 (mp0) REVERT: D 413 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8871 (mmmm) REVERT: D 414 GLU cc_start: 0.9337 (mp0) cc_final: 0.8169 (mp0) REVERT: D 421 LEU cc_start: 0.8177 (mt) cc_final: 0.7930 (mt) REVERT: D 431 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8106 (tm-30) REVERT: D 469 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8751 (mm-30) REVERT: D 472 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8305 (tm-30) REVERT: D 473 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8726 (mt) REVERT: D 476 PHE cc_start: 0.8739 (m-10) cc_final: 0.8207 (m-10) REVERT: D 522 GLN cc_start: 0.8636 (mt0) cc_final: 0.8402 (mt0) REVERT: E 413 LYS cc_start: 0.9047 (tppp) cc_final: 0.8736 (tmtt) REVERT: E 438 VAL cc_start: 0.8506 (t) cc_final: 0.8269 (m) REVERT: E 474 LYS cc_start: 0.9271 (mttt) cc_final: 0.8999 (mttm) REVERT: F 479 TYR cc_start: 0.8039 (m-80) cc_final: 0.7609 (m-80) REVERT: F 522 GLN cc_start: 0.8752 (mt0) cc_final: 0.8250 (mm-40) REVERT: F 524 LEU cc_start: 0.8204 (tt) cc_final: 0.7605 (pp) REVERT: G 423 GLN cc_start: 0.9393 (tm-30) cc_final: 0.9138 (tm-30) REVERT: G 424 ILE cc_start: 0.8920 (pt) cc_final: 0.8626 (pt) REVERT: G 468 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8247 (ttp80) REVERT: G 479 TYR cc_start: 0.7883 (m-80) cc_final: 0.7449 (m-80) REVERT: G 497 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8403 (ptp90) REVERT: G 521 GLN cc_start: 0.9140 (tt0) cc_final: 0.8568 (pp30) REVERT: H 413 LYS cc_start: 0.9141 (tppp) cc_final: 0.8838 (tppp) REVERT: H 431 GLU cc_start: 0.9295 (tt0) cc_final: 0.9072 (tm-30) REVERT: H 486 ASN cc_start: 0.9347 (t0) cc_final: 0.8971 (t0) REVERT: H 522 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8135 (tp-100) REVERT: H 545 MET cc_start: 0.5934 (ptt) cc_final: 0.5523 (ptt) outliers start: 29 outliers final: 20 residues processed: 375 average time/residue: 0.3080 time to fit residues: 152.7031 Evaluate side-chains 378 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 355 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 454 ASP 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 C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 417 VAL 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 437 GLN 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 G residue 447 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 495 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 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** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.127546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.088633 restraints weight = 146695.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.095754 restraints weight = 40662.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.100955 restraints weight = 21259.027| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10140 Z= 0.186 Angle : 0.867 11.641 13664 Z= 0.430 Chirality : 0.047 0.215 1484 Planarity : 0.005 0.039 1767 Dihedral : 8.610 179.793 1462 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.02 % Allowed : 30.23 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1201 helix: -0.05 (0.19), residues: 765 sheet: None (None), residues: 0 loop : 0.48 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 490 HIS 0.007 0.001 HIS F 530 PHE 0.013 0.001 PHE H 476 TYR 0.022 0.002 TYR E 501 ARG 0.011 0.001 ARG G 484 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 485) hydrogen bonds : angle 5.29881 ( 1327) covalent geometry : bond 0.00440 (10132) covalent geometry : angle 0.86666 (13664) Misc. bond : bond 0.00065 ( 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 397 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 364 time to evaluate : 1.209 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: A 411 SER cc_start: 0.8183 (m) cc_final: 0.7931 (t) REVERT: A 454 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7239 (t0) REVERT: A 472 GLU cc_start: 0.8189 (tp30) cc_final: 0.7824 (tp30) REVERT: A 476 PHE cc_start: 0.8544 (m-10) cc_final: 0.8314 (m-10) REVERT: A 478 ASN cc_start: 0.8747 (t0) cc_final: 0.8516 (t0) REVERT: A 479 TYR cc_start: 0.8619 (m-80) cc_final: 0.8298 (m-80) REVERT: A 497 ARG cc_start: 0.8737 (mtm180) cc_final: 0.8429 (ptp90) REVERT: A 503 TYR cc_start: 0.8874 (t80) cc_final: 0.8588 (t80) REVERT: A 522 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8180 (mm-40) REVERT: A 525 GLU cc_start: 0.9129 (mp0) cc_final: 0.8516 (mp0) REVERT: A 529 ILE cc_start: 0.8394 (mt) cc_final: 0.7938 (tt) REVERT: A 530 HIS cc_start: 0.8632 (m90) cc_final: 0.8185 (m-70) REVERT: B 450 GLU cc_start: 0.9054 (mp0) cc_final: 0.8735 (pm20) REVERT: B 452 GLN cc_start: 0.8968 (pp30) cc_final: 0.8648 (tm-30) REVERT: B 457 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6653 (mmm) REVERT: B 489 ASP cc_start: 0.9188 (m-30) cc_final: 0.8892 (t0) REVERT: B 490 TRP cc_start: 0.8204 (t-100) cc_final: 0.7843 (t-100) REVERT: B 503 TYR cc_start: 0.8453 (t80) cc_final: 0.8059 (t80) REVERT: B 517 ARG cc_start: 0.9248 (ttt-90) cc_final: 0.9030 (mtp85) REVERT: B 521 GLN cc_start: 0.8664 (mm110) cc_final: 0.8309 (pp30) REVERT: C 474 LYS cc_start: 0.9295 (mttt) cc_final: 0.9088 (mttp) REVERT: C 479 TYR cc_start: 0.8335 (m-80) cc_final: 0.7807 (m-80) REVERT: C 490 TRP cc_start: 0.8546 (t-100) cc_final: 0.8229 (t-100) REVERT: C 525 GLU cc_start: 0.8849 (mp0) cc_final: 0.8314 (mp0) REVERT: D 421 LEU cc_start: 0.8450 (mt) cc_final: 0.8213 (mt) REVERT: D 431 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8148 (tm-30) REVERT: D 469 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8799 (mm-30) REVERT: D 472 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8251 (tm-30) REVERT: D 473 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8746 (mp) REVERT: D 476 PHE cc_start: 0.8848 (m-10) cc_final: 0.8311 (m-10) REVERT: D 522 GLN cc_start: 0.8721 (mt0) cc_final: 0.8507 (mt0) REVERT: E 413 LYS cc_start: 0.9095 (tppp) cc_final: 0.8755 (tmtt) REVERT: E 438 VAL cc_start: 0.8664 (t) cc_final: 0.8414 (m) REVERT: E 450 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8606 (mt-10) REVERT: E 497 ARG cc_start: 0.9128 (mtm180) cc_final: 0.8673 (ptp90) REVERT: E 525 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8282 (mm-30) REVERT: F 451 LEU cc_start: 0.8917 (tp) cc_final: 0.8703 (tp) REVERT: F 479 TYR cc_start: 0.8191 (m-80) cc_final: 0.7697 (m-80) REVERT: F 522 GLN cc_start: 0.8829 (mt0) cc_final: 0.8314 (mm-40) REVERT: G 424 ILE cc_start: 0.8900 (pt) cc_final: 0.8675 (pt) REVERT: G 479 TYR cc_start: 0.7984 (m-80) cc_final: 0.7572 (m-80) REVERT: G 497 ARG cc_start: 0.8926 (mtm-85) cc_final: 0.8646 (ptp90) REVERT: G 521 GLN cc_start: 0.9216 (tt0) cc_final: 0.8623 (pp30) REVERT: H 413 LYS cc_start: 0.9180 (tppp) cc_final: 0.8911 (tppp) REVERT: H 431 GLU cc_start: 0.9340 (tt0) cc_final: 0.8914 (tm-30) REVERT: H 486 ASN cc_start: 0.9378 (t0) cc_final: 0.8990 (t0) REVERT: H 522 GLN cc_start: 0.8786 (mm-40) cc_final: 0.7997 (mm-40) outliers start: 33 outliers final: 24 residues processed: 382 average time/residue: 0.2699 time to fit residues: 137.0453 Evaluate side-chains 380 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 353 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 473 LEU 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 467 PHE 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 437 GLN 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 518 VAL Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 495 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 500 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS F 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.127065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087594 restraints weight = 170909.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.094803 restraints weight = 43288.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.100079 restraints weight = 22336.188| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10140 Z= 0.178 Angle : 0.899 12.322 13664 Z= 0.443 Chirality : 0.048 0.221 1484 Planarity : 0.004 0.039 1767 Dihedral : 8.579 179.984 1462 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.84 % Allowed : 30.59 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1201 helix: -0.08 (0.19), residues: 765 sheet: None (None), residues: 0 loop : 0.45 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 490 HIS 0.007 0.001 HIS E 530 PHE 0.013 0.001 PHE E 476 TYR 0.020 0.003 TYR F 429 ARG 0.010 0.001 ARG G 484 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 485) hydrogen bonds : angle 5.31300 ( 1327) covalent geometry : bond 0.00431 (10132) covalent geometry : angle 0.89894 (13664) Misc. bond : bond 0.00065 ( 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 400 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 369 time to evaluate : 1.222 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: A 411 SER cc_start: 0.8137 (m) cc_final: 0.7888 (t) REVERT: A 454 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7165 (t0) REVERT: A 478 ASN cc_start: 0.8694 (t0) cc_final: 0.8360 (t0) REVERT: A 487 LEU cc_start: 0.8934 (mt) cc_final: 0.8681 (mt) REVERT: A 497 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8477 (ptp90) REVERT: A 503 TYR cc_start: 0.8882 (t80) cc_final: 0.8617 (t80) REVERT: A 522 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8152 (mm-40) REVERT: A 530 HIS cc_start: 0.8661 (m90) cc_final: 0.8206 (m-70) REVERT: B 450 GLU cc_start: 0.9111 (mp0) cc_final: 0.8846 (pm20) REVERT: B 489 ASP cc_start: 0.9174 (m-30) cc_final: 0.8843 (t0) REVERT: B 490 TRP cc_start: 0.8143 (t-100) cc_final: 0.7802 (t-100) REVERT: B 503 TYR cc_start: 0.8462 (t80) cc_final: 0.8109 (t80) REVERT: B 517 ARG cc_start: 0.9264 (ttt-90) cc_final: 0.9060 (mtp85) REVERT: B 521 GLN cc_start: 0.8648 (mm110) cc_final: 0.8384 (pp30) REVERT: B 522 GLN cc_start: 0.8688 (tp40) cc_final: 0.8305 (tp40) REVERT: C 424 ILE cc_start: 0.8585 (pt) cc_final: 0.8381 (pt) REVERT: C 479 TYR cc_start: 0.8363 (m-80) cc_final: 0.7903 (m-80) REVERT: C 490 TRP cc_start: 0.8589 (t-100) cc_final: 0.8223 (t-100) REVERT: C 525 GLU cc_start: 0.8856 (mp0) cc_final: 0.8298 (mp0) REVERT: D 413 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8884 (mmmm) REVERT: D 414 GLU cc_start: 0.9327 (mp0) cc_final: 0.8234 (mp0) REVERT: D 431 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8041 (tm-30) REVERT: D 472 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8300 (tm-30) REVERT: D 473 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8925 (mt) REVERT: D 476 PHE cc_start: 0.8822 (m-10) cc_final: 0.8297 (m-10) REVERT: E 438 VAL cc_start: 0.8635 (t) cc_final: 0.8375 (m) REVERT: E 450 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8642 (mt-10) REVERT: E 497 ARG cc_start: 0.9157 (mtm180) cc_final: 0.8719 (ptp90) REVERT: E 543 ARG cc_start: 0.9005 (mmt90) cc_final: 0.8369 (ptt180) REVERT: F 451 LEU cc_start: 0.9013 (tp) cc_final: 0.8799 (tp) REVERT: F 479 TYR cc_start: 0.8129 (m-80) cc_final: 0.7691 (m-80) REVERT: F 522 GLN cc_start: 0.8827 (mt0) cc_final: 0.8292 (mm-40) REVERT: G 413 LYS cc_start: 0.8820 (tmtt) cc_final: 0.8619 (tmtt) REVERT: G 414 GLU cc_start: 0.9390 (mp0) cc_final: 0.8755 (mp0) REVERT: G 479 TYR cc_start: 0.8071 (m-80) cc_final: 0.7824 (m-80) REVERT: G 497 ARG cc_start: 0.8947 (mtm-85) cc_final: 0.8673 (ptp90) REVERT: G 521 GLN cc_start: 0.9198 (tt0) cc_final: 0.8628 (pp30) REVERT: H 413 LYS cc_start: 0.9146 (tppp) cc_final: 0.8860 (tppp) REVERT: H 431 GLU cc_start: 0.9321 (tt0) cc_final: 0.8981 (tm-30) REVERT: H 486 ASN cc_start: 0.9348 (t0) cc_final: 0.8995 (t0) REVERT: H 503 TYR cc_start: 0.8775 (t80) cc_final: 0.8567 (t80) REVERT: H 520 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7943 (tm-30) REVERT: H 522 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8205 (tp-100) REVERT: H 545 MET cc_start: 0.5823 (ptt) cc_final: 0.5583 (ptt) outliers start: 31 outliers final: 23 residues processed: 382 average time/residue: 0.2675 time to fit residues: 138.9375 Evaluate side-chains 378 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 353 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 454 ASP 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 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 473 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain F residue 403 ARG 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 518 VAL Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 0.0970 chunk 33 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 0.0030 chunk 107 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.129187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089440 restraints weight = 174277.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.096799 restraints weight = 42493.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.102108 restraints weight = 21809.281| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.7402 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= 0.173 Angle : 0.939 13.212 13664 Z= 0.460 Chirality : 0.048 0.243 1484 Planarity : 0.004 0.045 1767 Dihedral : 8.530 179.966 1460 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.20 % Allowed : 31.51 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1201 helix: -0.13 (0.19), residues: 764 sheet: None (None), residues: 0 loop : 0.32 (0.34), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 490 HIS 0.015 0.001 HIS F 530 PHE 0.017 0.001 PHE B 476 TYR 0.045 0.003 TYR B 501 ARG 0.009 0.001 ARG G 484 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 485) hydrogen bonds : angle 5.30845 ( 1327) covalent geometry : bond 0.00417 (10132) covalent geometry : angle 0.93895 (13664) Misc. bond : bond 0.00045 ( 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 394 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 370 time to evaluate : 1.269 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: A 411 SER cc_start: 0.8094 (m) cc_final: 0.7852 (t) REVERT: A 454 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7202 (t0) REVERT: A 478 ASN cc_start: 0.8738 (t0) cc_final: 0.8493 (t0) REVERT: A 479 TYR cc_start: 0.8509 (m-80) cc_final: 0.8261 (m-80) REVERT: A 487 LEU cc_start: 0.8920 (mt) cc_final: 0.8671 (mt) REVERT: A 497 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8467 (ptp90) REVERT: A 503 TYR cc_start: 0.8814 (t80) cc_final: 0.8520 (t80) REVERT: A 522 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8087 (mm-40) REVERT: A 530 HIS cc_start: 0.8650 (m90) cc_final: 0.8172 (m-70) REVERT: B 450 GLU cc_start: 0.9040 (mp0) cc_final: 0.8775 (pm20) REVERT: B 489 ASP cc_start: 0.9199 (m-30) cc_final: 0.8924 (t0) REVERT: B 490 TRP cc_start: 0.8110 (t-100) cc_final: 0.7803 (t-100) REVERT: B 522 GLN cc_start: 0.8635 (tp40) cc_final: 0.8319 (tp-100) REVERT: B 529 ILE cc_start: 0.7175 (mm) cc_final: 0.6901 (mm) REVERT: C 479 TYR cc_start: 0.8301 (m-80) cc_final: 0.7833 (m-80) REVERT: C 490 TRP cc_start: 0.8566 (t-100) cc_final: 0.8168 (t-100) REVERT: C 520 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 521 GLN cc_start: 0.8361 (pp30) cc_final: 0.7788 (pp30) REVERT: C 525 GLU cc_start: 0.8847 (mp0) cc_final: 0.8250 (mp0) REVERT: D 413 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8886 (mmmm) REVERT: D 414 GLU cc_start: 0.9337 (mp0) cc_final: 0.8255 (mp0) REVERT: D 431 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 472 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8280 (tm-30) REVERT: D 473 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8903 (mt) REVERT: D 476 PHE cc_start: 0.8790 (m-10) cc_final: 0.8273 (m-10) REVERT: E 438 VAL cc_start: 0.8697 (t) cc_final: 0.8462 (m) REVERT: E 450 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8629 (mt-10) REVERT: E 457 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6580 (mmm) REVERT: E 497 ARG cc_start: 0.9153 (mtm180) cc_final: 0.8744 (ptp90) REVERT: F 451 LEU cc_start: 0.9017 (tp) cc_final: 0.8801 (tp) REVERT: F 479 TYR cc_start: 0.8054 (m-80) cc_final: 0.7587 (m-80) REVERT: F 522 GLN cc_start: 0.8802 (mt0) cc_final: 0.8318 (mm-40) REVERT: F 524 LEU cc_start: 0.8238 (tt) cc_final: 0.7606 (pp) REVERT: G 414 GLU cc_start: 0.9390 (mp0) cc_final: 0.8888 (mp0) REVERT: G 431 GLU cc_start: 0.8863 (tp30) cc_final: 0.8580 (tm-30) REVERT: G 479 TYR cc_start: 0.7908 (m-80) cc_final: 0.7675 (m-80) REVERT: G 497 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8621 (ptp90) REVERT: G 521 GLN cc_start: 0.9133 (tt0) cc_final: 0.8543 (pp30) REVERT: H 431 GLU cc_start: 0.9325 (tt0) cc_final: 0.9009 (tm-30) REVERT: H 450 GLU cc_start: 0.9124 (mp0) cc_final: 0.8745 (pm20) REVERT: H 486 ASN cc_start: 0.9321 (t0) cc_final: 0.8963 (t0) REVERT: H 501 TYR cc_start: 0.8514 (m-80) cc_final: 0.8130 (m-80) REVERT: H 503 TYR cc_start: 0.8686 (t80) cc_final: 0.8470 (t80) REVERT: H 520 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7930 (tm-30) REVERT: H 522 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8301 (tp-100) REVERT: H 545 MET cc_start: 0.5623 (ptt) cc_final: 0.5409 (ptt) outliers start: 24 outliers final: 16 residues processed: 381 average time/residue: 0.2970 time to fit residues: 154.5154 Evaluate side-chains 372 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 353 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 454 ASP 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 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 473 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 457 MET 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 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 518 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 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 = 0.4159 r_free = 0.4159 target = 0.127673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089629 restraints weight = 166021.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096643 restraints weight = 40844.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.101798 restraints weight = 21010.653| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 10140 Z= 0.336 Angle : 1.198 59.164 13664 Z= 0.659 Chirality : 0.056 0.866 1484 Planarity : 0.007 0.203 1767 Dihedral : 8.526 179.997 1460 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.83 % Allowed : 31.96 % Favored : 65.21 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1201 helix: -0.14 (0.19), residues: 764 sheet: None (None), residues: 0 loop : 0.32 (0.33), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 420 HIS 0.324 0.007 HIS F 530 PHE 0.013 0.001 PHE B 476 TYR 0.119 0.004 TYR D 429 ARG 0.010 0.001 ARG F 484 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 485) hydrogen bonds : angle 5.30943 ( 1327) covalent geometry : bond 0.00689 (10132) covalent geometry : angle 1.19767 (13664) Misc. bond : bond 0.00052 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5408.85 seconds wall clock time: 98 minutes 7.01 seconds (5887.01 seconds total)