Starting phenix.real_space_refine on Fri Feb 14 04:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zg1_11191/02_2025/6zg1_11191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zg1_11191/02_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_11191/02_2025/6zg1_11191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zg1_11191/02_2025/6zg1_11191.map" model { file = "/net/cci-nas-00/data/ceres_data/6zg1_11191/02_2025/6zg1_11191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zg1_11191/02_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-5592/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: 10.54, per 1000 atoms: 1.06 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: 2.55 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: 1.22 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: 2.79 Time building geometry restraints manager: 2.79 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: 30.680 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- 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 10132 Z= 0.624 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 *********************** 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 : 1.031 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: 0.3080 time to fit residues: 241.1442 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 : 1.158 ------------------------------------------------------------------------------- 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 = 0.142011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099336 restraints weight = 138354.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.108040 restraints weight = 37567.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.114423 restraints weight = 19115.761| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 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 = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3925 ------------------------------------------------------------------------------- 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 10132 Z= 0.271 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 : 14.62 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 *********************** 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 : 1.007 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: 0.6181 (OUTLIER) cc_final: 0.5824 (mm) REVERT: A 411 SER cc_start: 0.8235 (m) cc_final: 0.7816 (t) REVERT: A 414 GLU cc_start: 0.8877 (mp0) cc_final: 0.8547 (mp0) REVERT: A 416 GLU cc_start: 0.9385 (mp0) cc_final: 0.9105 (mp0) REVERT: A 476 PHE cc_start: 0.8938 (m-10) cc_final: 0.8715 (m-10) REVERT: A 503 TYR cc_start: 0.8707 (t80) cc_final: 0.8425 (t80) REVERT: A 525 GLU cc_start: 0.9040 (mp0) cc_final: 0.8814 (mp0) REVERT: B 435 GLU cc_start: 0.9565 (tm-30) cc_final: 0.9205 (pp20) REVERT: B 479 TYR cc_start: 0.8172 (m-80) cc_final: 0.7678 (m-10) REVERT: B 490 TRP cc_start: 0.8148 (t-100) cc_final: 0.7790 (t-100) REVERT: B 503 TYR cc_start: 0.8148 (t80) cc_final: 0.7858 (t80) REVERT: B 520 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7841 (tm-30) REVERT: C 479 TYR cc_start: 0.7920 (m-80) cc_final: 0.7505 (m-80) REVERT: C 484 ARG cc_start: 0.9042 (ttm110) cc_final: 0.8767 (tmm160) REVERT: C 520 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 525 GLU cc_start: 0.8866 (mp0) cc_final: 0.8442 (mp0) REVERT: D 412 TRP cc_start: 0.7603 (m-10) cc_final: 0.7103 (m-10) REVERT: D 421 LEU cc_start: 0.8331 (mt) cc_final: 0.8068 (mt) REVERT: D 431 GLU cc_start: 0.8649 (tm-30) cc_final: 0.7940 (tm-30) REVERT: D 434 ARG cc_start: 0.8041 (tmm-80) cc_final: 0.7552 (tmm-80) REVERT: D 444 LEU cc_start: 0.8694 (mt) cc_final: 0.8471 (mt) REVERT: D 478 ASN cc_start: 0.7849 (t0) cc_final: 0.7634 (t0) REVERT: D 497 ARG cc_start: 0.8509 (mtm110) cc_final: 0.8200 (ptm160) REVERT: D 531 LEU cc_start: 0.6244 (tp) cc_final: 0.5992 (tp) REVERT: E 414 GLU cc_start: 0.8794 (mp0) cc_final: 0.8582 (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: 0.8121 (m) REVERT: E 449 GLU cc_start: 0.8582 (tp30) cc_final: 0.8212 (tp30) REVERT: E 486 ASN cc_start: 0.9501 (t0) cc_final: 0.9301 (t0) REVERT: E 503 TYR cc_start: 0.8204 (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: 0.9373 (tp) cc_final: 0.9171 (mp) REVERT: F 476 PHE cc_start: 0.9138 (m-80) cc_final: 0.8796 (m-10) REVERT: F 479 TYR cc_start: 0.7802 (m-80) cc_final: 0.7446 (m-80) REVERT: F 531 LEU cc_start: 0.6946 (mt) cc_final: 0.6460 (tp) REVERT: G 414 GLU cc_start: 0.8407 (mp0) cc_final: 0.8132 (mm-30) REVERT: G 474 LYS cc_start: 0.9441 (mttt) cc_final: 0.9229 (mttp) REVERT: G 476 PHE cc_start: 0.9082 (m-80) cc_final: 0.8521 (m-10) REVERT: G 479 TYR cc_start: 0.8052 (m-80) cc_final: 0.7657 (m-80) REVERT: G 515 LEU cc_start: 0.9633 (tp) cc_final: 0.9411 (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: 0.7252 (ptp) cc_final: 0.6897 (ptt) REVERT: H 431 GLU cc_start: 0.9151 (tt0) cc_final: 0.8930 (tm-30) REVERT: H 438 VAL cc_start: 0.8187 (t) cc_final: 0.7963 (m) REVERT: H 476 PHE cc_start: 0.8886 (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: 0.2801 time to fit residues: 161.5478 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 : 1.175 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 516 HIS ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN H 530 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.131299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.091666 restraints weight = 152061.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.099284 restraints weight = 38941.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.104852 restraints weight = 19782.001| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 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 = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10132 Z= 0.296 Angle : 0.830 10.076 13664 Z= 0.422 Chirality : 0.046 0.171 1484 Planarity : 0.005 0.056 1767 Dihedral : 9.675 179.898 1467 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.84 % Allowed : 25.66 % Favored : 69.50 % 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: 0.24 (0.25), residues: 1201 helix: -0.04 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 0.93 (0.34), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 490 HIS 0.018 0.002 HIS B 530 PHE 0.023 0.002 PHE B 476 TYR 0.020 0.003 TYR E 501 ARG 0.008 0.001 ARG F 445 *********************** 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 417 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 375 time to evaluate : 1.263 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: 0.6339 (OUTLIER) cc_final: 0.5975 (mm) REVERT: A 411 SER cc_start: 0.8342 (m) cc_final: 0.8008 (t) REVERT: A 414 GLU cc_start: 0.8762 (mp0) cc_final: 0.8308 (mp0) REVERT: A 416 GLU cc_start: 0.9343 (mp0) cc_final: 0.9098 (mp0) REVERT: A 476 PHE cc_start: 0.8920 (m-10) cc_final: 0.8719 (m-10) REVERT: A 478 ASN cc_start: 0.8794 (t0) cc_final: 0.8545 (t0) REVERT: A 503 TYR cc_start: 0.8854 (t80) cc_final: 0.8511 (t80) REVERT: A 522 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7672 (mm-40) REVERT: A 529 ILE cc_start: 0.8455 (mt) cc_final: 0.7974 (tt) REVERT: B 414 GLU cc_start: 0.9325 (mp0) cc_final: 0.9051 (pm20) REVERT: B 435 GLU cc_start: 0.9587 (tm-30) cc_final: 0.9239 (pp20) REVERT: B 438 VAL cc_start: 0.8467 (t) cc_final: 0.8086 (m) REVERT: B 449 GLU cc_start: 0.8561 (tp30) cc_final: 0.8302 (tp30) REVERT: B 450 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8627 (mt-10) REVERT: B 452 GLN cc_start: 0.8466 (pp30) cc_final: 0.8218 (tm-30) REVERT: B 479 TYR cc_start: 0.8269 (m-80) cc_final: 0.7815 (m-10) REVERT: B 489 ASP cc_start: 0.9205 (m-30) cc_final: 0.8877 (t0) REVERT: B 490 TRP cc_start: 0.8220 (t-100) cc_final: 0.7858 (t-100) REVERT: B 503 TYR cc_start: 0.8438 (t80) cc_final: 0.7954 (t80) REVERT: C 468 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6880 (mtm-85) REVERT: C 474 LYS cc_start: 0.9163 (mttm) cc_final: 0.8901 (mttt) REVERT: C 479 TYR cc_start: 0.8250 (m-80) cc_final: 0.7715 (m-80) REVERT: C 484 ARG cc_start: 0.8994 (ttm110) cc_final: 0.8725 (tmm160) REVERT: C 490 TRP cc_start: 0.8635 (t-100) cc_final: 0.8191 (t-100) REVERT: C 521 GLN cc_start: 0.8272 (pp30) cc_final: 0.7744 (pp30) REVERT: C 522 GLN cc_start: 0.8532 (mt0) cc_final: 0.8039 (mp10) REVERT: C 525 GLU cc_start: 0.8783 (mp0) cc_final: 0.8283 (mp0) REVERT: D 414 GLU cc_start: 0.9168 (mp0) cc_final: 0.8743 (mp0) REVERT: D 421 LEU cc_start: 0.8458 (mt) cc_final: 0.8234 (mt) REVERT: D 431 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 449 GLU cc_start: 0.8810 (pp20) cc_final: 0.8485 (pp20) REVERT: D 472 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8308 (tp30) REVERT: D 476 PHE cc_start: 0.8867 (m-10) cc_final: 0.7803 (m-10) REVERT: D 497 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8207 (ptp-170) REVERT: D 545 MET cc_start: 0.4395 (ptm) cc_final: 0.4175 (ptm) REVERT: E 413 LYS cc_start: 0.9147 (tppp) cc_final: 0.8719 (tmtt) REVERT: E 435 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9365 (pp20) REVERT: E 438 VAL cc_start: 0.8494 (t) cc_final: 0.8276 (m) REVERT: E 449 GLU cc_start: 0.8586 (tp30) cc_final: 0.8348 (tp30) REVERT: E 503 TYR cc_start: 0.8374 (t80) cc_final: 0.8072 (t80) REVERT: F 479 TYR cc_start: 0.8069 (m-80) cc_final: 0.7663 (m-80) REVERT: F 483 ASP cc_start: 0.8095 (t0) cc_final: 0.7853 (t0) REVERT: G 479 TYR cc_start: 0.8011 (m-80) cc_final: 0.7804 (m-80) REVERT: G 522 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7606 (mm-40) REVERT: H 413 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8498 (tptp) REVERT: H 418 GLN cc_start: 0.8916 (mm110) cc_final: 0.8471 (mm110) REVERT: H 431 GLU cc_start: 0.9216 (tt0) cc_final: 0.8965 (tm-30) REVERT: H 438 VAL cc_start: 0.8442 (t) cc_final: 0.8196 (m) REVERT: H 476 PHE cc_start: 0.8888 (m-80) cc_final: 0.8444 (m-10) REVERT: H 545 MET cc_start: 0.5851 (ptt) cc_final: 0.5373 (ptt) outliers start: 42 outliers final: 25 residues processed: 392 average time/residue: 0.2740 time to fit residues: 140.5570 Evaluate side-chains 365 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 338 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 C residue 529 ILE 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 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 523 LEU 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: 4.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** 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 500 GLN F 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.131578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090614 restraints weight = 165244.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.098323 restraints weight = 40719.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.104031 restraints weight = 20780.873| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10132 Z= 0.250 Angle : 0.836 14.495 13664 Z= 0.415 Chirality : 0.047 0.235 1484 Planarity : 0.005 0.054 1767 Dihedral : 9.253 179.997 1464 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.20 % Allowed : 27.95 % Favored : 67.85 % 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: 0.21 (0.25), residues: 1201 helix: 0.06 (0.18), residues: 771 sheet: None (None), residues: 0 loop : 0.66 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 490 HIS 0.006 0.001 HIS F 530 PHE 0.016 0.001 PHE B 476 TYR 0.030 0.002 TYR F 429 ARG 0.009 0.001 ARG G 484 *********************** 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 407 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 372 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6550 (mm) REVERT: A 411 SER cc_start: 0.8314 (m) cc_final: 0.8043 (t) REVERT: A 414 GLU cc_start: 0.8728 (mp0) cc_final: 0.8310 (mm-30) REVERT: A 444 LEU cc_start: 0.8789 (mt) cc_final: 0.8539 (mt) REVERT: A 454 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6886 (t0) REVERT: A 476 PHE cc_start: 0.8827 (m-10) cc_final: 0.8460 (m-10) REVERT: A 478 ASN cc_start: 0.8736 (t0) cc_final: 0.8398 (t0) REVERT: A 503 TYR cc_start: 0.8787 (t80) cc_final: 0.8421 (t80) REVERT: A 530 HIS cc_start: 0.8641 (m90) cc_final: 0.8346 (m-70) REVERT: B 413 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8685 (tmtt) REVERT: B 435 GLU cc_start: 0.9567 (tm-30) cc_final: 0.9224 (pp20) REVERT: B 438 VAL cc_start: 0.8413 (t) cc_final: 0.8195 (m) REVERT: B 452 GLN cc_start: 0.8501 (pp30) cc_final: 0.8198 (tm-30) REVERT: B 464 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8792 (ttmt) REVERT: B 479 TYR cc_start: 0.8278 (m-80) cc_final: 0.7953 (m-10) REVERT: B 489 ASP cc_start: 0.9168 (m-30) cc_final: 0.8848 (t0) REVERT: B 490 TRP cc_start: 0.8110 (t-100) cc_final: 0.7709 (t-100) REVERT: C 468 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7025 (mtm-85) REVERT: C 479 TYR cc_start: 0.8109 (m-80) cc_final: 0.7441 (m-80) REVERT: C 490 TRP cc_start: 0.8594 (t-100) cc_final: 0.8238 (t-100) REVERT: C 520 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 521 GLN cc_start: 0.8231 (pp30) cc_final: 0.7789 (pp30) REVERT: C 522 GLN cc_start: 0.8426 (mt0) cc_final: 0.8155 (mp10) REVERT: C 525 GLU cc_start: 0.8889 (mp0) cc_final: 0.8411 (mp0) REVERT: D 414 GLU cc_start: 0.9155 (mp0) cc_final: 0.8657 (mp0) REVERT: D 421 LEU cc_start: 0.8300 (mt) cc_final: 0.8039 (mt) REVERT: D 431 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 454 ASP cc_start: 0.7686 (t0) cc_final: 0.7395 (t0) REVERT: D 472 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8319 (tp30) REVERT: D 476 PHE cc_start: 0.8814 (m-10) cc_final: 0.7982 (m-10) REVERT: D 497 ARG cc_start: 0.8520 (mtm110) cc_final: 0.8113 (ptp-170) REVERT: D 517 ARG cc_start: 0.9383 (mmm-85) cc_final: 0.9101 (mmm160) REVERT: D 522 GLN cc_start: 0.8646 (mt0) cc_final: 0.8338 (mm-40) REVERT: E 435 GLU cc_start: 0.9584 (tm-30) cc_final: 0.9313 (pp20) REVERT: E 438 VAL cc_start: 0.8474 (t) cc_final: 0.8240 (m) REVERT: E 449 GLU cc_start: 0.8600 (tp30) cc_final: 0.8388 (tp30) REVERT: E 543 ARG cc_start: 0.8806 (mmt90) cc_final: 0.8086 (mtm110) REVERT: F 426 PHE cc_start: 0.6609 (m-80) cc_final: 0.6343 (m-10) REVERT: F 429 TYR cc_start: 0.8581 (m-80) cc_final: 0.8211 (m-80) REVERT: F 479 TYR cc_start: 0.7956 (m-80) cc_final: 0.7493 (m-80) REVERT: G 479 TYR cc_start: 0.8018 (m-80) cc_final: 0.7777 (m-80) REVERT: G 522 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7515 (mm-40) REVERT: H 418 GLN cc_start: 0.8860 (mm110) cc_final: 0.8200 (mm110) REVERT: H 431 GLU cc_start: 0.9240 (tt0) cc_final: 0.8948 (tm-30) REVERT: H 438 VAL cc_start: 0.8514 (t) cc_final: 0.8258 (m) REVERT: H 522 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8325 (tp-100) REVERT: H 545 MET cc_start: 0.5485 (ptt) cc_final: 0.5143 (ptt) outliers start: 35 outliers final: 23 residues processed: 390 average time/residue: 0.2641 time to fit residues: 136.0201 Evaluate side-chains 362 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 336 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 468 ARG Chi-restraints excluded: chain C residue 516 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 467 PHE 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 F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR 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: 0.0570 chunk 76 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 1.5900 ------------------------------------------------------------------------------- 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 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.129745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.089576 restraints weight = 159961.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097061 restraints weight = 39996.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.102550 restraints weight = 20449.170| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10132 Z= 0.256 Angle : 0.826 17.677 13664 Z= 0.410 Chirality : 0.046 0.249 1484 Planarity : 0.004 0.041 1767 Dihedral : 9.052 179.782 1464 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.93 % Allowed : 28.31 % Favored : 67.76 % 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: 0.19 (0.25), residues: 1201 helix: 0.03 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.66 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 490 HIS 0.022 0.001 HIS F 530 PHE 0.016 0.001 PHE H 476 TYR 0.028 0.003 TYR E 429 ARG 0.009 0.001 ARG D 543 *********************** 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 392 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 360 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6778 (mm) REVERT: A 411 SER cc_start: 0.8281 (m) cc_final: 0.8020 (t) REVERT: A 414 GLU cc_start: 0.8709 (mp0) cc_final: 0.8276 (mp0) REVERT: A 444 LEU cc_start: 0.8786 (mt) cc_final: 0.8539 (mt) REVERT: A 454 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.7049 (t0) REVERT: A 476 PHE cc_start: 0.8833 (m-10) cc_final: 0.8474 (m-10) REVERT: A 478 ASN cc_start: 0.8770 (t0) cc_final: 0.8408 (t0) REVERT: A 503 TYR cc_start: 0.8772 (t80) cc_final: 0.8418 (t80) REVERT: A 529 ILE cc_start: 0.8463 (mt) cc_final: 0.8060 (tt) REVERT: B 452 GLN cc_start: 0.8740 (pp30) cc_final: 0.8416 (tm-30) REVERT: B 464 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8814 (ttmt) REVERT: B 479 TYR cc_start: 0.8349 (m-80) cc_final: 0.8016 (m-10) REVERT: B 489 ASP cc_start: 0.9191 (m-30) cc_final: 0.8862 (t0) REVERT: B 490 TRP cc_start: 0.8147 (t-100) cc_final: 0.7752 (t-100) REVERT: B 503 TYR cc_start: 0.8309 (t80) cc_final: 0.8092 (t80) REVERT: B 521 GLN cc_start: 0.8506 (mm110) cc_final: 0.7927 (pp30) REVERT: C 479 TYR cc_start: 0.8233 (m-80) cc_final: 0.7707 (m-80) REVERT: C 490 TRP cc_start: 0.8596 (t-100) cc_final: 0.8318 (t-100) REVERT: C 520 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8028 (tm-30) REVERT: C 521 GLN cc_start: 0.8289 (pp30) cc_final: 0.7885 (pp30) REVERT: C 525 GLU cc_start: 0.8935 (mp0) cc_final: 0.8417 (mp0) REVERT: D 421 LEU cc_start: 0.8307 (mt) cc_final: 0.8052 (mt) REVERT: D 431 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8090 (tm-30) REVERT: D 469 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8544 (mm-30) REVERT: D 472 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8372 (tm-30) REVERT: D 473 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8762 (mt) REVERT: D 476 PHE cc_start: 0.8851 (m-10) cc_final: 0.8332 (m-10) REVERT: D 522 GLN cc_start: 0.8732 (mt0) cc_final: 0.8414 (mm-40) REVERT: E 413 LYS cc_start: 0.9067 (tppp) cc_final: 0.8701 (tmtt) REVERT: E 438 VAL cc_start: 0.8530 (t) cc_final: 0.8314 (m) REVERT: F 479 TYR cc_start: 0.8059 (m-80) cc_final: 0.7598 (m-80) REVERT: F 522 GLN cc_start: 0.8779 (mt0) cc_final: 0.8185 (mm-40) REVERT: G 479 TYR cc_start: 0.8012 (m-80) cc_final: 0.7615 (m-80) REVERT: G 497 ARG cc_start: 0.8884 (mtm-85) cc_final: 0.8469 (ptp90) REVERT: G 522 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7577 (mm-40) REVERT: H 418 GLN cc_start: 0.8885 (mm110) cc_final: 0.8309 (mm110) REVERT: H 431 GLU cc_start: 0.9265 (tt0) cc_final: 0.8958 (tm-30) REVERT: H 438 VAL cc_start: 0.8535 (t) cc_final: 0.8290 (m) REVERT: H 486 ASN cc_start: 0.9364 (t0) cc_final: 0.9008 (t0) REVERT: H 545 MET cc_start: 0.5385 (ptt) cc_final: 0.5051 (ptt) outliers start: 32 outliers final: 23 residues processed: 380 average time/residue: 0.2551 time to fit residues: 129.1504 Evaluate side-chains 364 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 338 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 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 G residue 417 VAL Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR 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: 2.9990 chunk 108 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 15 optimal weight: 0.0050 chunk 7 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0996 ------------------------------------------------------------------------------- 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** C 436 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 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS F 534 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.130006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.090498 restraints weight = 151139.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.097913 restraints weight = 39827.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103307 restraints weight = 20476.148| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10132 Z= 0.252 Angle : 0.847 14.212 13664 Z= 0.421 Chirality : 0.046 0.224 1484 Planarity : 0.004 0.041 1767 Dihedral : 8.899 179.925 1464 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.02 % Allowed : 30.32 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.18), residues: 770 sheet: None (None), residues: 0 loop : 0.54 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 490 HIS 0.022 0.001 HIS E 530 PHE 0.017 0.001 PHE B 476 TYR 0.025 0.002 TYR E 501 ARG 0.009 0.001 ARG G 484 *********************** 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 397 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 364 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.8239 (m) cc_final: 0.7967 (t) REVERT: A 414 GLU cc_start: 0.8694 (mp0) cc_final: 0.8392 (mp0) REVERT: A 444 LEU cc_start: 0.8768 (mt) cc_final: 0.8562 (mt) REVERT: A 446 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 450 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8758 (pp20) REVERT: A 454 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6929 (t0) REVERT: A 476 PHE cc_start: 0.8843 (m-10) cc_final: 0.8474 (m-10) REVERT: A 478 ASN cc_start: 0.8673 (t0) cc_final: 0.8307 (t0) REVERT: A 503 TYR cc_start: 0.8718 (t80) cc_final: 0.8428 (t80) REVERT: A 530 HIS cc_start: 0.8662 (m90) cc_final: 0.8200 (m-70) REVERT: A 544 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8712 (mm-30) REVERT: B 452 GLN cc_start: 0.8842 (pp30) cc_final: 0.8533 (tm-30) REVERT: B 457 MET cc_start: 0.6686 (mmm) cc_final: 0.6119 (mmm) REVERT: B 479 TYR cc_start: 0.8373 (m-80) cc_final: 0.8151 (m-10) REVERT: B 489 ASP cc_start: 0.9161 (m-30) cc_final: 0.8849 (t0) REVERT: B 490 TRP cc_start: 0.8128 (t-100) cc_final: 0.7732 (t-100) REVERT: B 521 GLN cc_start: 0.8598 (mm110) cc_final: 0.8213 (pp30) REVERT: B 522 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8014 (tp-100) REVERT: C 424 ILE cc_start: 0.8507 (pt) cc_final: 0.8297 (pt) REVERT: C 479 TYR cc_start: 0.8223 (m-80) cc_final: 0.7692 (m-80) REVERT: C 490 TRP cc_start: 0.8562 (t-100) cc_final: 0.8246 (t-100) REVERT: C 520 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7871 (tm-30) REVERT: C 521 GLN cc_start: 0.8301 (pp30) cc_final: 0.7582 (pp30) REVERT: C 525 GLU cc_start: 0.8918 (mp0) cc_final: 0.8372 (mp0) REVERT: D 413 LYS cc_start: 0.9186 (tmtt) cc_final: 0.8864 (mmmm) REVERT: D 414 GLU cc_start: 0.9335 (mp0) cc_final: 0.8127 (mp0) REVERT: D 421 LEU cc_start: 0.8251 (mt) cc_final: 0.7992 (mt) REVERT: D 431 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8080 (tm-30) REVERT: D 449 GLU cc_start: 0.8946 (pp20) cc_final: 0.8278 (pp20) REVERT: D 450 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9154 (mp0) REVERT: D 472 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8350 (tm-30) REVERT: D 473 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8884 (mt) REVERT: D 476 PHE cc_start: 0.8809 (m-10) cc_final: 0.8279 (m-10) REVERT: D 522 GLN cc_start: 0.8735 (mt0) cc_final: 0.8507 (mt0) REVERT: D 525 GLU cc_start: 0.9128 (mp0) cc_final: 0.8734 (mp0) REVERT: E 413 LYS cc_start: 0.9074 (tppp) cc_final: 0.8730 (tmtt) REVERT: E 438 VAL cc_start: 0.8592 (t) cc_final: 0.8344 (m) REVERT: F 426 PHE cc_start: 0.6657 (m-80) cc_final: 0.6295 (m-10) REVERT: F 479 TYR cc_start: 0.8049 (m-80) cc_final: 0.7524 (m-80) REVERT: F 522 GLN cc_start: 0.8761 (mt0) cc_final: 0.8244 (mm-40) REVERT: F 524 LEU cc_start: 0.8275 (tt) cc_final: 0.7793 (pp) REVERT: G 468 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8198 (ttp80) REVERT: G 479 TYR cc_start: 0.7991 (m-80) cc_final: 0.7616 (m-80) REVERT: G 497 ARG cc_start: 0.8823 (mtm-85) cc_final: 0.8451 (ptp90) REVERT: G 522 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7557 (mm-40) REVERT: H 431 GLU cc_start: 0.9293 (tt0) cc_final: 0.9040 (tm-30) REVERT: H 438 VAL cc_start: 0.8599 (t) cc_final: 0.8326 (m) REVERT: H 486 ASN cc_start: 0.9376 (t0) cc_final: 0.8999 (t0) REVERT: H 522 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8069 (mm-40) REVERT: H 545 MET cc_start: 0.5648 (ptt) cc_final: 0.5359 (ptt) outliers start: 33 outliers final: 23 residues processed: 382 average time/residue: 0.2611 time to fit residues: 133.4230 Evaluate side-chains 381 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 446 LEU 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 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 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 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 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** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.129286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.089992 restraints weight = 158607.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097304 restraints weight = 40775.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.102693 restraints weight = 20960.919| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10132 Z= 0.256 Angle : 0.859 12.063 13664 Z= 0.422 Chirality : 0.047 0.319 1484 Planarity : 0.005 0.044 1767 Dihedral : 8.719 179.927 1462 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.84 % Allowed : 30.50 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.19), residues: 766 sheet: None (None), residues: 0 loop : 0.53 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 490 HIS 0.010 0.001 HIS F 530 PHE 0.014 0.001 PHE B 476 TYR 0.017 0.002 TYR B 503 ARG 0.010 0.001 ARG G 484 *********************** 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 397 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 366 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.8235 (m) cc_final: 0.7974 (t) REVERT: A 414 GLU cc_start: 0.8747 (mp0) cc_final: 0.8342 (mp0) REVERT: A 450 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8764 (pp20) REVERT: A 454 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7126 (t0) REVERT: A 472 GLU cc_start: 0.8483 (tp30) cc_final: 0.8132 (tm-30) REVERT: A 476 PHE cc_start: 0.8854 (m-10) cc_final: 0.8591 (m-10) REVERT: A 478 ASN cc_start: 0.8690 (t0) cc_final: 0.8347 (t0) REVERT: A 503 TYR cc_start: 0.8742 (t80) cc_final: 0.8380 (t80) REVERT: A 525 GLU cc_start: 0.9095 (mp0) cc_final: 0.8761 (mp0) REVERT: A 530 HIS cc_start: 0.8677 (m90) cc_final: 0.8228 (m-70) REVERT: A 544 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8761 (mm-30) REVERT: B 451 LEU cc_start: 0.8937 (tp) cc_final: 0.8696 (tp) REVERT: B 452 GLN cc_start: 0.8897 (pp30) cc_final: 0.8595 (tm-30) REVERT: B 457 MET cc_start: 0.7154 (mmm) cc_final: 0.6534 (mmm) REVERT: B 479 TYR cc_start: 0.8331 (m-80) cc_final: 0.8111 (m-10) REVERT: B 489 ASP cc_start: 0.9176 (m-30) cc_final: 0.8909 (t0) REVERT: B 490 TRP cc_start: 0.8175 (t-100) cc_final: 0.7801 (t-100) REVERT: B 503 TYR cc_start: 0.8213 (t80) cc_final: 0.7805 (t80) REVERT: B 521 GLN cc_start: 0.8614 (mm110) cc_final: 0.8283 (pp30) REVERT: C 474 LYS cc_start: 0.9280 (mttt) cc_final: 0.9067 (mttp) REVERT: C 479 TYR cc_start: 0.8208 (m-80) cc_final: 0.7662 (m-80) REVERT: C 490 TRP cc_start: 0.8487 (t-100) cc_final: 0.8183 (t-100) REVERT: C 520 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 525 GLU cc_start: 0.8898 (mp0) cc_final: 0.8340 (mp0) REVERT: D 413 LYS cc_start: 0.9169 (tmtt) cc_final: 0.8908 (mmmm) REVERT: D 414 GLU cc_start: 0.9320 (mp0) cc_final: 0.8060 (mp0) REVERT: D 421 LEU cc_start: 0.8274 (mt) cc_final: 0.8021 (mt) REVERT: D 431 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 449 GLU cc_start: 0.9018 (pp20) cc_final: 0.8320 (pp20) REVERT: D 450 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9052 (mp0) REVERT: D 472 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8342 (tm-30) REVERT: D 473 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8936 (mt) REVERT: D 476 PHE cc_start: 0.8818 (m-10) cc_final: 0.8247 (m-10) REVERT: D 522 GLN cc_start: 0.8670 (mt0) cc_final: 0.8420 (mt0) REVERT: D 525 GLU cc_start: 0.9140 (mp0) cc_final: 0.8756 (mp0) REVERT: E 413 LYS cc_start: 0.9061 (tppp) cc_final: 0.8738 (tmtt) REVERT: E 438 VAL cc_start: 0.8623 (t) cc_final: 0.8358 (m) REVERT: E 497 ARG cc_start: 0.9092 (mtm180) cc_final: 0.8631 (ptp90) REVERT: F 479 TYR cc_start: 0.8103 (m-80) cc_final: 0.7645 (m-80) REVERT: F 522 GLN cc_start: 0.8782 (mt0) cc_final: 0.8275 (mm-40) REVERT: F 524 LEU cc_start: 0.8302 (tt) cc_final: 0.7679 (pp) REVERT: G 423 GLN cc_start: 0.9417 (tm-30) cc_final: 0.9159 (tm-30) REVERT: G 424 ILE cc_start: 0.8969 (pt) cc_final: 0.8681 (pt) REVERT: G 468 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8265 (ttp80) REVERT: G 479 TYR cc_start: 0.7970 (m-80) cc_final: 0.7537 (m-80) REVERT: G 497 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8461 (ptp90) REVERT: G 521 GLN cc_start: 0.9149 (tt0) cc_final: 0.8570 (pp30) REVERT: H 413 LYS cc_start: 0.9143 (tppp) cc_final: 0.8879 (tppp) REVERT: H 431 GLU cc_start: 0.9321 (tt0) cc_final: 0.9085 (tm-30) REVERT: H 486 ASN cc_start: 0.9331 (t0) cc_final: 0.8980 (t0) REVERT: H 520 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7931 (tm-30) REVERT: H 522 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8036 (mm-40) REVERT: H 545 MET cc_start: 0.6034 (ptt) cc_final: 0.5812 (ptt) outliers start: 31 outliers final: 24 residues processed: 382 average time/residue: 0.2628 time to fit residues: 132.8333 Evaluate side-chains 379 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 352 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 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 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 518 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 73 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.128729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.089745 restraints weight = 146144.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.096903 restraints weight = 40032.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.102141 restraints weight = 20797.112| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 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 = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.7109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10132 Z= 0.268 Angle : 0.873 12.390 13664 Z= 0.432 Chirality : 0.047 0.296 1484 Planarity : 0.004 0.039 1767 Dihedral : 8.628 179.943 1462 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.93 % Allowed : 30.32 % 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: -0.03 (0.25), residues: 1201 helix: -0.14 (0.19), residues: 766 sheet: None (None), residues: 0 loop : 0.57 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 490 HIS 0.029 0.001 HIS F 530 PHE 0.009 0.001 PHE B 476 TYR 0.017 0.002 TYR H 479 ARG 0.011 0.001 ARG G 484 *********************** 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: 32 poor density : 365 time to evaluate : 1.059 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: 0.8247 (m) cc_final: 0.7963 (t) REVERT: A 414 GLU cc_start: 0.8669 (mp0) cc_final: 0.8389 (mp0) REVERT: A 416 GLU cc_start: 0.9266 (mp0) cc_final: 0.9008 (mp0) REVERT: A 454 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7112 (t0) REVERT: A 472 GLU cc_start: 0.8501 (tp30) cc_final: 0.8162 (tm-30) REVERT: A 476 PHE cc_start: 0.8875 (m-10) cc_final: 0.8606 (m-10) REVERT: A 478 ASN cc_start: 0.8723 (t0) cc_final: 0.8392 (t0) REVERT: A 497 ARG cc_start: 0.8648 (mtm180) cc_final: 0.8328 (ptp90) REVERT: A 503 TYR cc_start: 0.8804 (t80) cc_final: 0.8479 (t80) REVERT: A 522 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7552 (mm-40) REVERT: A 530 HIS cc_start: 0.8690 (m90) cc_final: 0.8234 (m-70) REVERT: B 449 GLU cc_start: 0.8899 (tp30) cc_final: 0.8686 (tp30) REVERT: B 450 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8792 (pt0) REVERT: B 451 LEU cc_start: 0.8996 (tp) cc_final: 0.8792 (tp) REVERT: B 452 GLN cc_start: 0.8924 (pp30) cc_final: 0.8582 (tm-30) REVERT: B 457 MET cc_start: 0.7186 (mmm) cc_final: 0.6550 (mmm) REVERT: B 479 TYR cc_start: 0.8351 (m-80) cc_final: 0.8122 (m-10) REVERT: B 490 TRP cc_start: 0.8151 (t-100) cc_final: 0.7802 (t-100) REVERT: B 503 TYR cc_start: 0.8372 (t80) cc_final: 0.7942 (t80) REVERT: B 521 GLN cc_start: 0.8679 (mm110) cc_final: 0.8358 (pp30) REVERT: C 479 TYR cc_start: 0.8215 (m-80) cc_final: 0.7674 (m-80) REVERT: C 490 TRP cc_start: 0.8527 (t-100) cc_final: 0.8192 (t-100) REVERT: C 520 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7823 (tm-30) REVERT: C 525 GLU cc_start: 0.8870 (mp0) cc_final: 0.8333 (mp0) REVERT: D 413 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8885 (mmmm) REVERT: D 414 GLU cc_start: 0.9317 (mp0) cc_final: 0.8086 (mp0) REVERT: D 431 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8084 (tm-30) REVERT: D 449 GLU cc_start: 0.9089 (pp20) cc_final: 0.8541 (pp20) REVERT: D 450 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9087 (mp0) REVERT: D 469 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8672 (mm-30) REVERT: D 472 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8328 (tm-30) REVERT: D 473 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8933 (mt) REVERT: D 476 PHE cc_start: 0.8805 (m-10) cc_final: 0.8259 (m-10) REVERT: D 522 GLN cc_start: 0.8713 (mt0) cc_final: 0.8337 (mm-40) REVERT: E 413 LYS cc_start: 0.9083 (tppp) cc_final: 0.8703 (tmtt) REVERT: E 438 VAL cc_start: 0.8644 (t) cc_final: 0.8395 (m) REVERT: E 497 ARG cc_start: 0.9103 (mtm180) cc_final: 0.8663 (ptp90) REVERT: F 451 LEU cc_start: 0.8933 (tp) cc_final: 0.8703 (tp) REVERT: F 479 TYR cc_start: 0.8163 (m-80) cc_final: 0.7670 (m-80) REVERT: F 522 GLN cc_start: 0.8796 (mt0) cc_final: 0.8304 (mm-40) REVERT: F 524 LEU cc_start: 0.8246 (tt) cc_final: 0.7581 (pp) REVERT: G 423 GLN cc_start: 0.9431 (tm-30) cc_final: 0.9211 (tm-30) REVERT: G 424 ILE cc_start: 0.8875 (pt) cc_final: 0.8625 (pt) REVERT: G 450 GLU cc_start: 0.9290 (mp0) cc_final: 0.9087 (pm20) REVERT: G 479 TYR cc_start: 0.8007 (m-80) cc_final: 0.7649 (m-80) REVERT: G 497 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8444 (ptp90) REVERT: G 521 GLN cc_start: 0.9190 (tt0) cc_final: 0.8617 (pp30) REVERT: H 431 GLU cc_start: 0.9335 (tt0) cc_final: 0.8906 (tm-30) REVERT: H 484 ARG cc_start: 0.8247 (ttp80) cc_final: 0.8047 (pmt-80) REVERT: H 486 ASN cc_start: 0.9346 (t0) cc_final: 0.9000 (t0) REVERT: H 520 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7940 (tm-30) REVERT: H 522 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8018 (mm-40) outliers start: 32 outliers final: 24 residues processed: 383 average time/residue: 0.2539 time to fit residues: 129.3984 Evaluate side-chains 379 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 353 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 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 516 HIS 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 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 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 518 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 522 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** F 530 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.128012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.088907 restraints weight = 168545.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.096091 restraints weight = 42219.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.101356 restraints weight = 21619.125| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10132 Z= 0.265 Angle : 0.877 12.307 13664 Z= 0.433 Chirality : 0.046 0.221 1484 Planarity : 0.004 0.037 1767 Dihedral : 8.545 179.902 1462 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.47 % Allowed : 30.59 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.25), residues: 1201 helix: -0.15 (0.19), residues: 765 sheet: None (None), residues: 0 loop : 0.52 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 490 HIS 0.005 0.001 HIS B 534 PHE 0.013 0.001 PHE H 476 TYR 0.019 0.002 TYR F 429 ARG 0.010 0.001 ARG G 484 *********************** 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 399 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 372 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: symmetry clash revert: symmetry clash REVERT: A 450 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8744 (pp20) REVERT: A 454 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7128 (t0) REVERT: A 472 GLU cc_start: 0.8530 (tp30) cc_final: 0.8204 (tm-30) REVERT: A 476 PHE cc_start: 0.8947 (m-10) cc_final: 0.8706 (m-10) REVERT: A 478 ASN cc_start: 0.8641 (t0) cc_final: 0.8325 (t0) REVERT: A 497 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8406 (ptp90) REVERT: A 503 TYR cc_start: 0.8819 (t80) cc_final: 0.8496 (t80) REVERT: A 522 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7851 (mm-40) REVERT: A 525 GLU cc_start: 0.9090 (mp0) cc_final: 0.8771 (mp0) REVERT: A 530 HIS cc_start: 0.8694 (m90) cc_final: 0.8232 (m-70) REVERT: B 449 GLU cc_start: 0.8935 (tp30) cc_final: 0.8714 (tp30) REVERT: B 450 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8400 (pt0) REVERT: B 452 GLN cc_start: 0.8873 (pp30) cc_final: 0.8527 (tm-30) REVERT: B 457 MET cc_start: 0.7334 (mmm) cc_final: 0.6691 (mmm) REVERT: B 489 ASP cc_start: 0.9191 (m-30) cc_final: 0.8873 (t0) REVERT: B 490 TRP cc_start: 0.8126 (t-100) cc_final: 0.7768 (t-100) REVERT: B 503 TYR cc_start: 0.8469 (t80) cc_final: 0.8219 (t80) REVERT: B 530 HIS cc_start: 0.8350 (m90) cc_final: 0.8093 (m-70) REVERT: C 479 TYR cc_start: 0.8230 (m-80) cc_final: 0.7697 (m-80) REVERT: C 490 TRP cc_start: 0.8565 (t-100) cc_final: 0.8204 (t-100) REVERT: C 520 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 525 GLU cc_start: 0.8835 (mp0) cc_final: 0.8283 (mp0) REVERT: D 414 GLU cc_start: 0.9321 (mp0) cc_final: 0.8779 (mp0) REVERT: D 431 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 449 GLU cc_start: 0.9161 (pp20) cc_final: 0.8403 (pp20) REVERT: D 450 GLU cc_start: 0.9270 (mt-10) cc_final: 0.9020 (mp0) REVERT: D 469 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8775 (mm-30) REVERT: D 472 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8294 (tm-30) REVERT: D 473 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8914 (mt) REVERT: D 476 PHE cc_start: 0.8797 (m-10) cc_final: 0.8258 (m-10) REVERT: E 438 VAL cc_start: 0.8702 (t) cc_final: 0.8421 (m) REVERT: E 457 MET cc_start: 0.7343 (mmt) cc_final: 0.7004 (mmt) REVERT: E 497 ARG cc_start: 0.9142 (mtm180) cc_final: 0.8720 (ptp90) REVERT: E 543 ARG cc_start: 0.9003 (mmt90) cc_final: 0.8368 (ptt180) REVERT: F 451 LEU cc_start: 0.9019 (tp) cc_final: 0.8795 (tp) REVERT: F 479 TYR cc_start: 0.8077 (m-80) cc_final: 0.7621 (m-80) REVERT: F 522 GLN cc_start: 0.8799 (mt0) cc_final: 0.8307 (mm-40) REVERT: F 524 LEU cc_start: 0.8246 (tt) cc_final: 0.7593 (pp) REVERT: G 413 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8446 (mtpp) REVERT: G 414 GLU cc_start: 0.9362 (mp0) cc_final: 0.8365 (mp0) REVERT: G 423 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9215 (tm-30) REVERT: G 424 ILE cc_start: 0.8903 (pt) cc_final: 0.8685 (pt) REVERT: G 474 LYS cc_start: 0.9202 (mttt) cc_final: 0.8879 (mttp) REVERT: G 479 TYR cc_start: 0.8042 (m-80) cc_final: 0.7819 (m-80) REVERT: G 497 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8427 (ptp90) REVERT: G 521 GLN cc_start: 0.9145 (tt0) cc_final: 0.8546 (pp30) REVERT: H 431 GLU cc_start: 0.9325 (tt0) cc_final: 0.9013 (tm-30) REVERT: H 484 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7931 (pmt-80) REVERT: H 486 ASN cc_start: 0.9339 (t0) cc_final: 0.8994 (t0) REVERT: H 520 GLU cc_start: 0.8259 (tm-30) cc_final: 0.8005 (tm-30) REVERT: H 522 GLN cc_start: 0.8768 (mm-40) cc_final: 0.7997 (mm-40) REVERT: H 545 MET cc_start: 0.5867 (ptt) cc_final: 0.5642 (ptt) outliers start: 27 outliers final: 22 residues processed: 384 average time/residue: 0.2525 time to fit residues: 129.4138 Evaluate side-chains 381 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 357 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER 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 516 HIS 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 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 G residue 447 THR Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.126334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.087324 restraints weight = 176096.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.094502 restraints weight = 43190.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.099659 restraints weight = 22038.119| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.7519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10132 Z= 0.277 Angle : 0.905 13.367 13664 Z= 0.445 Chirality : 0.048 0.305 1484 Planarity : 0.004 0.036 1767 Dihedral : 8.485 179.971 1460 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.11 % Allowed : 31.60 % 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: -0.12 (0.25), residues: 1201 helix: -0.17 (0.19), residues: 765 sheet: None (None), residues: 0 loop : 0.44 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 490 HIS 0.008 0.001 HIS F 530 PHE 0.011 0.001 PHE E 466 TYR 0.034 0.002 TYR E 503 ARG 0.009 0.001 ARG G 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 369 time to evaluate : 1.083 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 414 GLU cc_start: 0.9033 (mp0) cc_final: 0.8613 (mp0) REVERT: A 444 LEU cc_start: 0.8954 (mp) cc_final: 0.8643 (mp) REVERT: A 454 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7378 (t0) REVERT: A 472 GLU cc_start: 0.8510 (tp30) cc_final: 0.8224 (tm-30) REVERT: A 476 PHE cc_start: 0.8983 (m-10) cc_final: 0.8738 (m-10) REVERT: A 478 ASN cc_start: 0.8714 (t0) cc_final: 0.8409 (t0) REVERT: A 497 ARG cc_start: 0.8809 (mtm180) cc_final: 0.8517 (ptp90) REVERT: A 503 TYR cc_start: 0.8888 (t80) cc_final: 0.8600 (t80) REVERT: A 522 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7577 (mm-40) REVERT: A 525 GLU cc_start: 0.9117 (mp0) cc_final: 0.8808 (mp0) REVERT: A 530 HIS cc_start: 0.8654 (m90) cc_final: 0.8206 (m-70) REVERT: B 450 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8453 (pt0) REVERT: B 489 ASP cc_start: 0.9253 (m-30) cc_final: 0.9008 (t0) REVERT: B 490 TRP cc_start: 0.8125 (t-100) cc_final: 0.7801 (t-100) REVERT: B 503 TYR cc_start: 0.8653 (t80) cc_final: 0.8308 (t80) REVERT: B 530 HIS cc_start: 0.8349 (m90) cc_final: 0.8091 (m-70) REVERT: C 479 TYR cc_start: 0.8426 (m-80) cc_final: 0.7972 (m-80) REVERT: C 490 TRP cc_start: 0.8594 (t-100) cc_final: 0.8198 (t-100) REVERT: C 495 ASP cc_start: 0.8356 (t0) cc_final: 0.8058 (t70) REVERT: C 520 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 521 GLN cc_start: 0.8412 (pp30) cc_final: 0.7937 (pp30) REVERT: C 525 GLU cc_start: 0.8853 (mp0) cc_final: 0.8283 (mp0) REVERT: D 413 LYS cc_start: 0.9159 (tmtt) cc_final: 0.8950 (mtpp) REVERT: D 431 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8000 (tm-30) REVERT: D 469 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8824 (mm-30) REVERT: D 472 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8343 (tm-30) REVERT: D 473 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8929 (mt) REVERT: D 476 PHE cc_start: 0.8839 (m-10) cc_final: 0.8335 (m-10) REVERT: D 522 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8075 (mt0) REVERT: E 438 VAL cc_start: 0.8763 (t) cc_final: 0.8487 (m) REVERT: E 497 ARG cc_start: 0.9179 (mtm180) cc_final: 0.8773 (ptp90) REVERT: E 543 ARG cc_start: 0.9028 (mmt90) cc_final: 0.8411 (ptt180) REVERT: F 451 LEU cc_start: 0.9110 (tp) cc_final: 0.8891 (tp) REVERT: F 479 TYR cc_start: 0.8142 (m-80) cc_final: 0.7716 (m-80) REVERT: F 522 GLN cc_start: 0.8844 (mt0) cc_final: 0.8356 (mm-40) REVERT: F 524 LEU cc_start: 0.8219 (tt) cc_final: 0.7539 (pp) REVERT: G 413 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8505 (mtpp) REVERT: G 414 GLU cc_start: 0.9377 (mp0) cc_final: 0.8383 (mp0) REVERT: G 497 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8480 (ptp90) REVERT: G 521 GLN cc_start: 0.9161 (tt0) cc_final: 0.8553 (pp30) REVERT: H 431 GLU cc_start: 0.9354 (tt0) cc_final: 0.8987 (tm-30) REVERT: H 484 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7934 (pmt-80) REVERT: H 486 ASN cc_start: 0.9369 (t0) cc_final: 0.9022 (t0) REVERT: H 503 TYR cc_start: 0.8802 (t80) cc_final: 0.8577 (t80) REVERT: H 520 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8054 (tm-30) REVERT: H 522 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8065 (mm-40) outliers start: 23 outliers final: 18 residues processed: 378 average time/residue: 0.2451 time to fit residues: 124.3703 Evaluate side-chains 382 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 362 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 506 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 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 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 530 HIS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.127430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.088581 restraints weight = 167943.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.095703 restraints weight = 42059.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.100854 restraints weight = 21681.570| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10132 Z= 0.279 Angle : 0.925 14.263 13664 Z= 0.453 Chirality : 0.047 0.249 1484 Planarity : 0.004 0.036 1767 Dihedral : 8.466 179.956 1460 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.83 % Allowed : 32.69 % Favored : 64.47 % 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: -0.17 (0.25), residues: 1201 helix: -0.21 (0.19), residues: 763 sheet: None (None), residues: 0 loop : 0.42 (0.35), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 490 HIS 0.016 0.001 HIS F 530 PHE 0.019 0.001 PHE B 476 TYR 0.043 0.003 TYR B 501 ARG 0.009 0.001 ARG G 484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4638.09 seconds wall clock time: 83 minutes 41.91 seconds (5021.91 seconds total)