Starting phenix.real_space_refine on Wed Mar 4 01:12:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zg1_11191/03_2026/6zg1_11191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zg1_11191/03_2026/6zg1_11191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zg1_11191/03_2026/6zg1_11191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zg1_11191/03_2026/6zg1_11191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zg1_11191/03_2026/6zg1_11191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zg1_11191/03_2026/6zg1_11191.map" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 6232 2.51 5 N 1769 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9931 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1164 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 143, 1164 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} bond proxies already assigned to first conformer: 1132 Chain: "B" Number of atoms: 1324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1250 Chain: "C" Number of atoms: 1232 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1206 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 142} Conformer: "B" Number of residues, atoms: 148, 1206 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 142} bond proxies already assigned to first conformer: 1199 Chain: "D" Number of atoms: 1204 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} bond proxies already assigned to first conformer: 1200 Chain: "E" Number of atoms: 1209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} bond proxies already assigned to first conformer: 1196 Chain: "F" Number of atoms: 1211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1174 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 144, 1174 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} bond proxies already assigned to first conformer: 1152 Chain: "G" Number of atoms: 1206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 1181 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 145, 1181 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} bond proxies already assigned to first conformer: 1174 Chain: "H" Number of atoms: 1210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 140} Conformer: "B" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 140} bond proxies already assigned to first conformer: 1189 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {'BME': 1, 'EDO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {'BME': 1, 'EDO': 4, 'PEG': 1, 'PGE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 16 Unusual residues: {'BME': 1, 'EDO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 35 Unusual residues: {'BME': 1, 'EDO': 6, 'PEG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BME': 1, 'EDO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BME': 1, 'EDO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BME': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BME': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" C1 BME A 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME A 602 " occ=0.60 residue: pdb=" C1 EDO B 602 " occ=0.80 ... (2 atoms not shown) pdb=" O2 EDO B 602 " occ=0.80 residue: pdb=" C1 PEG B 603 " occ=0.80 ... (5 atoms not shown) pdb=" O4 PEG B 603 " occ=0.80 residue: pdb=" C1 BME B 604 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME B 604 " occ=0.60 residue: pdb=" C1 PGE B 605 " occ=0.70 ... (8 atoms not shown) pdb=" O4 PGE B 605 " occ=0.70 residue: pdb=" C1 BME C 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME C 601 " occ=0.60 residue: pdb=" C1 PEG D 602 " occ=0.80 ... (5 atoms not shown) pdb=" O4 PEG D 602 " occ=0.80 residue: pdb=" C1 BME D 603 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME D 603 " occ=0.60 residue: pdb=" C1 EDO D 606 " occ=0.80 ... (2 atoms not shown) pdb=" O2 EDO D 606 " occ=0.80 residue: pdb=" C1 BME E 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME E 602 " occ=0.60 residue: pdb=" C1 BME F 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME F 602 " occ=0.60 residue: pdb=" C1 BME G 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME G 601 " occ=0.60 residue: pdb=" C1 BME H 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME H 601 " occ=0.60 Time building chain proxies: 4.18, per 1000 atoms: 0.42 Number of scatterers: 9931 At special positions: 0 Unit cell: (121, 119.9, 69.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1866 8.00 N 1769 7.00 C 6232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 789.3 milliseconds 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.547A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.733A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.731A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 4.450A pdb=" N HIS A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 544 Processing helix chain 'B' and resid 394 through 398 removed outlier: 3.655A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.669A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.634A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 4.451A pdb=" N HIS B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 544 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 476 Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.517A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.523A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.667A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.455A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 544 removed outlier: 3.973A pdb=" N GLU C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 477 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.515A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.867A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.757A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 518 removed outlier: 4.715A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 544 removed outlier: 3.527A pdb=" N GLU D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 459 through 476 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.509A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.621A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.683A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 4.548A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 544 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 436 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 459 through 477 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.521A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.735A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.704A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 removed outlier: 4.441A pdb=" N HIS F 516 " --> pdb=" O ARG F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 544 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 459 through 476 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.524A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.714A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.716A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 516 removed outlier: 4.382A pdb=" N HIS G 516 " --> pdb=" O ARG G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 544 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 439 through 445 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 459 through 477 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.515A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.672A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.667A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 516 removed outlier: 4.435A pdb=" N HIS H 516 " --> pdb=" O ARG H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.656A pdb=" N GLU H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.22 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: 0.330 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 10140 Z= 0.638 Angle : 1.608 18.276 13664 Z= 1.047 Chirality : 0.105 0.670 1484 Planarity : 0.007 0.047 1767 Dihedral : 18.790 179.752 3943 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.98 % Favored : 97.93 % Rotamer: Outliers : 5.94 % Allowed : 6.58 % Favored : 87.49 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.21), residues: 1201 helix: -1.21 (0.16), residues: 768 sheet: None (None), residues: 0 loop : -0.26 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG F 468 TYR 0.041 0.009 TYR D 429 PHE 0.046 0.009 PHE E 476 TRP 0.034 0.008 TRP C 420 HIS 0.015 0.004 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00958 (10132) covalent geometry : angle 1.60849 (13664) hydrogen bonds : bond 0.19833 ( 485) hydrogen bonds : angle 6.68849 ( 1327) Misc. bond : bond 0.05001 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 593 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.4846 (OUTLIER) cc_final: 0.4345 (mm) REVERT: A 411 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.6795 (t) REVERT: A 424 ILE cc_start: 0.7374 (pt) cc_final: 0.6991 (pt) REVERT: B 411 SER cc_start: 0.6983 (OUTLIER) cc_final: 0.6696 (t) REVERT: C 447 THR cc_start: 0.7911 (p) cc_final: 0.7700 (p) REVERT: D 424 ILE cc_start: 0.7058 (pt) cc_final: 0.6573 (pt) REVERT: D 473 LEU cc_start: 0.7960 (tp) cc_final: 0.7751 (tp) REVERT: D 476 PHE cc_start: 0.7518 (m-80) cc_final: 0.7313 (m-10) REVERT: E 431 GLU cc_start: 0.7646 (tp30) cc_final: 0.7418 (tt0) REVERT: E 486 ASN cc_start: 0.7796 (t0) cc_final: 0.7479 (t0) REVERT: F 447 THR cc_start: 0.8170 (p) cc_final: 0.7720 (p) REVERT: F 524 LEU cc_start: 0.7482 (tp) cc_final: 0.7228 (tt) REVERT: G 411 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7446 (t) REVERT: G 424 ILE cc_start: 0.7777 (pt) cc_final: 0.7364 (pt) REVERT: H 431 GLU cc_start: 0.8665 (tt0) cc_final: 0.8237 (tm-30) outliers start: 54 outliers final: 8 residues processed: 618 average time/residue: 0.1247 time to fit residues: 98.0130 Evaluate side-chains 386 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 374 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain H residue 416 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D 516 HIS ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS E 534 HIS F 422 GLN F 530 HIS G 422 GLN G 436 GLN H 423 GLN H 452 GLN H 500 GLN H 530 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.137273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.095442 restraints weight = 141341.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.103779 restraints weight = 37770.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.109896 restraints weight = 19279.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.114285 restraints weight = 12036.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.117361 restraints weight = 8369.276| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10140 Z= 0.209 Angle : 0.856 9.772 13664 Z= 0.445 Chirality : 0.046 0.159 1484 Planarity : 0.006 0.060 1767 Dihedral : 10.220 178.278 1481 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.39 % Allowed : 22.65 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1201 helix: -0.23 (0.18), residues: 771 sheet: None (None), residues: 0 loop : 0.96 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 517 TYR 0.029 0.003 TYR E 501 PHE 0.024 0.002 PHE B 476 TRP 0.019 0.002 TRP C 490 HIS 0.009 0.002 HIS E 530 Details of bonding type rmsd covalent geometry : bond 0.00456 (10132) covalent geometry : angle 0.85647 (13664) hydrogen bonds : bond 0.05940 ( 485) hydrogen bonds : angle 5.28278 ( 1327) Misc. bond : bond 0.00158 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 418 time to evaluate : 0.398 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: 0.5784 (OUTLIER) cc_final: 0.5419 (mm) REVERT: A 411 SER cc_start: 0.8151 (m) cc_final: 0.7753 (t) REVERT: A 414 GLU cc_start: 0.8798 (mp0) cc_final: 0.8445 (mp0) REVERT: A 416 GLU cc_start: 0.9373 (mp0) cc_final: 0.9109 (mp0) REVERT: A 435 GLU cc_start: 0.9519 (tm-30) cc_final: 0.9282 (pp20) REVERT: A 503 TYR cc_start: 0.8680 (t80) cc_final: 0.8462 (t80) REVERT: A 525 GLU cc_start: 0.9066 (mp0) cc_final: 0.8856 (mp0) REVERT: B 438 VAL cc_start: 0.8225 (t) cc_final: 0.7903 (m) REVERT: B 449 GLU cc_start: 0.8537 (tp30) cc_final: 0.8267 (tp30) REVERT: B 479 TYR cc_start: 0.8257 (m-80) cc_final: 0.7736 (m-10) REVERT: B 489 ASP cc_start: 0.9028 (m-30) cc_final: 0.8762 (t0) REVERT: B 490 TRP cc_start: 0.8185 (t-100) cc_final: 0.7809 (t-100) REVERT: B 503 TYR cc_start: 0.8223 (t80) cc_final: 0.7846 (t80) REVERT: B 520 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7061 (tm-30) REVERT: C 479 TYR cc_start: 0.8042 (m-80) cc_final: 0.7652 (m-80) REVERT: C 484 ARG cc_start: 0.9022 (ttm110) cc_final: 0.8782 (tmm160) REVERT: C 520 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 525 GLU cc_start: 0.8881 (mp0) cc_final: 0.8434 (mp0) REVERT: D 412 TRP cc_start: 0.7651 (m-10) cc_final: 0.7122 (m-10) REVERT: D 431 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 444 LEU cc_start: 0.8681 (mt) cc_final: 0.8446 (mt) REVERT: D 472 GLU cc_start: 0.8300 (tp30) cc_final: 0.7776 (tp30) REVERT: D 476 PHE cc_start: 0.8784 (m-80) cc_final: 0.7962 (m-10) REVERT: D 497 ARG cc_start: 0.8518 (mtm110) cc_final: 0.8283 (ptm160) REVERT: D 522 GLN cc_start: 0.8640 (mt0) cc_final: 0.8406 (mm-40) REVERT: D 525 GLU cc_start: 0.9171 (mp0) cc_final: 0.8958 (mp0) REVERT: D 531 LEU cc_start: 0.6275 (tp) cc_final: 0.6044 (tp) REVERT: E 435 GLU cc_start: 0.9597 (tm-30) cc_final: 0.9312 (pp20) REVERT: E 438 VAL cc_start: 0.8428 (t) cc_final: 0.8125 (m) REVERT: E 449 GLU cc_start: 0.8638 (tp30) cc_final: 0.8294 (tp30) REVERT: E 503 TYR cc_start: 0.8230 (t80) cc_final: 0.7986 (t80) REVERT: F 476 PHE cc_start: 0.9161 (m-80) cc_final: 0.8799 (m-10) REVERT: F 479 TYR cc_start: 0.8027 (m-80) cc_final: 0.7741 (m-80) REVERT: F 483 ASP cc_start: 0.8018 (t0) cc_final: 0.7787 (t0) REVERT: G 414 GLU cc_start: 0.8481 (mp0) cc_final: 0.8265 (mm-30) REVERT: G 447 THR cc_start: 0.8145 (p) cc_final: 0.7774 (p) REVERT: G 476 PHE cc_start: 0.9094 (m-80) cc_final: 0.8506 (m-10) REVERT: G 479 TYR cc_start: 0.8056 (m-80) cc_final: 0.7828 (m-80) REVERT: G 503 TYR cc_start: 0.8598 (t80) cc_final: 0.8393 (t80) REVERT: G 522 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7401 (mm-40) REVERT: G 543 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8197 (mtm110) REVERT: G 545 MET cc_start: 0.7249 (ptp) cc_final: 0.7016 (ptt) REVERT: H 431 GLU cc_start: 0.9133 (tt0) cc_final: 0.8928 (tm-30) REVERT: H 447 THR cc_start: 0.7861 (p) cc_final: 0.6600 (p) REVERT: H 545 MET cc_start: 0.5941 (ptt) cc_final: 0.5325 (ptt) outliers start: 48 outliers final: 25 residues processed: 440 average time/residue: 0.1113 time to fit residues: 64.4849 Evaluate side-chains 369 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 343 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 530 HIS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 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 100 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 0.0470 chunk 71 optimal weight: 0.0060 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8098 ------------------------------------------------------------------------------- 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 500 GLN C 516 HIS ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 452 GLN H 530 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.134190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.094729 restraints weight = 145970.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.102505 restraints weight = 37876.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.108191 restraints weight = 19289.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.112245 restraints weight = 12005.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.115173 restraints weight = 8351.510| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10140 Z= 0.166 Angle : 0.831 10.502 13664 Z= 0.418 Chirality : 0.046 0.177 1484 Planarity : 0.005 0.054 1767 Dihedral : 9.466 179.798 1464 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.47 % Allowed : 26.58 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1201 helix: 0.04 (0.18), residues: 773 sheet: None (None), residues: 0 loop : 0.87 (0.34), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 484 TYR 0.020 0.003 TYR E 501 PHE 0.020 0.001 PHE B 476 TRP 0.026 0.002 TRP D 490 HIS 0.012 0.002 HIS B 530 Details of bonding type rmsd covalent geometry : bond 0.00375 (10132) covalent geometry : angle 0.83096 (13664) hydrogen bonds : bond 0.05090 ( 485) hydrogen bonds : angle 5.03131 ( 1327) Misc. bond : bond 0.00088 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 389 time to evaluate : 0.340 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: 0.5993 (OUTLIER) cc_final: 0.5615 (mm) REVERT: A 411 SER cc_start: 0.8135 (m) cc_final: 0.7729 (t) REVERT: A 414 GLU cc_start: 0.8744 (mp0) cc_final: 0.8238 (mm-30) REVERT: A 416 GLU cc_start: 0.9332 (mp0) cc_final: 0.9057 (mp0) REVERT: A 435 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9154 (pp20) REVERT: A 469 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8635 (mm-30) REVERT: A 478 ASN cc_start: 0.8728 (t0) cc_final: 0.8447 (t0) REVERT: A 503 TYR cc_start: 0.8689 (t80) cc_final: 0.8296 (t80) REVERT: A 522 GLN cc_start: 0.8511 (mm-40) cc_final: 0.7890 (mm-40) REVERT: B 413 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8592 (mmmm) REVERT: B 435 GLU cc_start: 0.9558 (tm-30) cc_final: 0.9181 (pp20) REVERT: B 438 VAL cc_start: 0.8127 (t) cc_final: 0.7860 (m) REVERT: B 457 MET cc_start: 0.6572 (mtp) cc_final: 0.6295 (ttm) REVERT: B 479 TYR cc_start: 0.8202 (m-80) cc_final: 0.7796 (m-10) REVERT: B 489 ASP cc_start: 0.9128 (m-30) cc_final: 0.8826 (t0) REVERT: B 490 TRP cc_start: 0.8185 (t-100) cc_final: 0.7816 (t-100) REVERT: B 503 TYR cc_start: 0.8315 (t80) cc_final: 0.7896 (t80) REVERT: C 468 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7002 (mtm-85) REVERT: C 474 LYS cc_start: 0.9000 (mttm) cc_final: 0.8762 (mmtt) REVERT: C 479 TYR cc_start: 0.8000 (m-80) cc_final: 0.7485 (m-80) REVERT: C 484 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8707 (tmm160) REVERT: C 521 GLN cc_start: 0.8209 (pp30) cc_final: 0.7878 (pp30) REVERT: C 525 GLU cc_start: 0.8835 (mp0) cc_final: 0.8542 (mp0) REVERT: D 414 GLU cc_start: 0.9173 (mp0) cc_final: 0.8745 (mp0) REVERT: D 431 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8058 (tm-30) REVERT: D 449 GLU cc_start: 0.8778 (pp20) cc_final: 0.8474 (pp20) REVERT: D 472 GLU cc_start: 0.8311 (tp30) cc_final: 0.7726 (tp30) REVERT: D 476 PHE cc_start: 0.8740 (m-80) cc_final: 0.7870 (m-10) REVERT: D 497 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8174 (ptp-170) REVERT: D 517 ARG cc_start: 0.9367 (mmm-85) cc_final: 0.9133 (mmm160) REVERT: D 525 GLU cc_start: 0.9163 (mp0) cc_final: 0.8941 (mp0) REVERT: D 545 MET cc_start: 0.3843 (ptm) cc_final: 0.3611 (ptm) REVERT: E 435 GLU cc_start: 0.9554 (tm-30) cc_final: 0.9306 (pp20) REVERT: E 449 GLU cc_start: 0.8495 (tp30) cc_final: 0.8213 (tp30) REVERT: E 503 TYR cc_start: 0.8200 (t80) cc_final: 0.7959 (t80) REVERT: F 413 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8554 (tmtt) REVERT: F 414 GLU cc_start: 0.8856 (mp0) cc_final: 0.8294 (mm-30) REVERT: F 426 PHE cc_start: 0.6264 (m-80) cc_final: 0.5919 (m-10) REVERT: F 457 MET cc_start: 0.6865 (mtt) cc_final: 0.6297 (mtp) REVERT: F 479 TYR cc_start: 0.7934 (m-80) cc_final: 0.7543 (m-80) REVERT: F 503 TYR cc_start: 0.8283 (t80) cc_final: 0.7987 (t80) REVERT: G 457 MET cc_start: 0.6779 (mtp) cc_final: 0.6501 (ttm) REVERT: G 503 TYR cc_start: 0.8800 (t80) cc_final: 0.8481 (t80) REVERT: G 522 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7420 (mm-40) REVERT: G 543 ARG cc_start: 0.8827 (mtt180) cc_final: 0.8212 (mtm110) REVERT: H 418 GLN cc_start: 0.8828 (mm110) cc_final: 0.8321 (mm110) REVERT: H 431 GLU cc_start: 0.9169 (tt0) cc_final: 0.8959 (tm-30) REVERT: H 545 MET cc_start: 0.5809 (ptt) cc_final: 0.5268 (ptt) outliers start: 27 outliers final: 16 residues processed: 405 average time/residue: 0.1138 time to fit residues: 60.3452 Evaluate side-chains 361 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 343 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 470 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.0370 chunk 104 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 452 GLN B 423 GLN C 436 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN H 530 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.132944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.092136 restraints weight = 164712.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.099900 restraints weight = 40330.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.105612 restraints weight = 20588.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.109660 restraints weight = 12906.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.112628 restraints weight = 9056.179| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10140 Z= 0.165 Angle : 0.835 15.098 13664 Z= 0.415 Chirality : 0.046 0.264 1484 Planarity : 0.005 0.102 1767 Dihedral : 9.260 179.901 1464 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.84 % Allowed : 27.67 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1201 helix: 0.03 (0.18), residues: 773 sheet: None (None), residues: 0 loop : 0.75 (0.34), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 535 TYR 0.018 0.002 TYR C 429 PHE 0.018 0.001 PHE G 476 TRP 0.012 0.001 TRP D 490 HIS 0.006 0.001 HIS E 530 Details of bonding type rmsd covalent geometry : bond 0.00384 (10132) covalent geometry : angle 0.83494 (13664) hydrogen bonds : bond 0.04811 ( 485) hydrogen bonds : angle 5.02964 ( 1327) Misc. bond : bond 0.00066 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 373 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.6465 (OUTLIER) cc_final: 0.6147 (mm) REVERT: A 411 SER cc_start: 0.8097 (m) cc_final: 0.7811 (t) REVERT: A 414 GLU cc_start: 0.8752 (mp0) cc_final: 0.8182 (mp0) REVERT: A 450 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8358 (pt0) REVERT: A 454 ASP cc_start: 0.7417 (m-30) cc_final: 0.7165 (t0) REVERT: A 469 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8625 (mm-30) REVERT: A 472 GLU cc_start: 0.8292 (tp30) cc_final: 0.7876 (tp30) REVERT: A 476 PHE cc_start: 0.8566 (m-10) cc_final: 0.8287 (m-10) REVERT: A 478 ASN cc_start: 0.8763 (t0) cc_final: 0.8405 (t0) REVERT: A 503 TYR cc_start: 0.8662 (t80) cc_final: 0.8273 (t80) REVERT: A 522 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7628 (mm-40) REVERT: A 525 GLU cc_start: 0.9062 (mp0) cc_final: 0.8764 (mp0) REVERT: A 529 ILE cc_start: 0.8208 (mt) cc_final: 0.7864 (tt) REVERT: B 435 GLU cc_start: 0.9562 (tm-30) cc_final: 0.9192 (pp20) REVERT: B 438 VAL cc_start: 0.8316 (t) cc_final: 0.8096 (m) REVERT: B 464 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8806 (ttmt) REVERT: B 479 TYR cc_start: 0.8281 (m-80) cc_final: 0.7911 (m-10) REVERT: B 489 ASP cc_start: 0.9119 (m-30) cc_final: 0.8791 (t0) REVERT: B 490 TRP cc_start: 0.8137 (t-100) cc_final: 0.7719 (t-100) REVERT: B 503 TYR cc_start: 0.8321 (t80) cc_final: 0.7885 (t80) REVERT: C 461 ILE cc_start: 0.8971 (tt) cc_final: 0.8747 (tt) REVERT: C 468 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7100 (mtm-85) REVERT: C 474 LYS cc_start: 0.9053 (mttm) cc_final: 0.8841 (mttt) REVERT: C 479 TYR cc_start: 0.8055 (m-80) cc_final: 0.7420 (m-80) REVERT: C 521 GLN cc_start: 0.8176 (pp30) cc_final: 0.7764 (pp30) REVERT: C 525 GLU cc_start: 0.8861 (mp0) cc_final: 0.8416 (mp0) REVERT: C 537 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7970 (mtp-110) REVERT: D 414 GLU cc_start: 0.9171 (mp0) cc_final: 0.8668 (mp0) REVERT: D 431 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8065 (tm-30) REVERT: D 454 ASP cc_start: 0.7691 (t0) cc_final: 0.7358 (t0) REVERT: D 472 GLU cc_start: 0.8408 (tp30) cc_final: 0.7767 (tp30) REVERT: D 476 PHE cc_start: 0.8699 (m-80) cc_final: 0.7808 (m-10) REVERT: D 497 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8116 (ptp-170) REVERT: D 517 ARG cc_start: 0.9316 (mmm-85) cc_final: 0.9076 (mmm160) REVERT: D 522 GLN cc_start: 0.8556 (mt0) cc_final: 0.8287 (mm-40) REVERT: D 525 GLU cc_start: 0.9163 (mp0) cc_final: 0.8920 (mp0) REVERT: E 429 TYR cc_start: 0.8008 (m-10) cc_final: 0.7771 (m-10) REVERT: E 435 GLU cc_start: 0.9565 (tm-30) cc_final: 0.9292 (pp20) REVERT: E 543 ARG cc_start: 0.8852 (mmt90) cc_final: 0.8073 (mtm110) REVERT: F 426 PHE cc_start: 0.6304 (m-80) cc_final: 0.5962 (m-10) REVERT: F 457 MET cc_start: 0.6832 (mtt) cc_final: 0.6309 (mtp) REVERT: F 479 TYR cc_start: 0.7997 (m-80) cc_final: 0.7610 (m-80) REVERT: G 503 TYR cc_start: 0.8771 (t80) cc_final: 0.8456 (t80) REVERT: G 522 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7440 (mm-40) REVERT: G 543 ARG cc_start: 0.8814 (mtt180) cc_final: 0.8193 (mtm110) REVERT: H 418 GLN cc_start: 0.8774 (mm110) cc_final: 0.8469 (mm110) REVERT: H 430 CYS cc_start: 0.8562 (t) cc_final: 0.8337 (m) REVERT: H 476 PHE cc_start: 0.9020 (m-10) cc_final: 0.8815 (m-10) REVERT: H 517 ARG cc_start: 0.9317 (ttt90) cc_final: 0.9021 (ttt-90) REVERT: H 545 MET cc_start: 0.5721 (ptt) cc_final: 0.5343 (ptt) outliers start: 31 outliers final: 24 residues processed: 392 average time/residue: 0.1120 time to fit residues: 57.6905 Evaluate side-chains 373 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 347 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 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 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 530 HIS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 461 ILE 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 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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** F 530 HIS ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN H 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.130114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090570 restraints weight = 158269.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.098015 restraints weight = 39645.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.103483 restraints weight = 20288.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.107439 restraints weight = 12730.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110321 restraints weight = 8915.076| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10140 Z= 0.173 Angle : 0.835 17.653 13664 Z= 0.414 Chirality : 0.047 0.280 1484 Planarity : 0.005 0.043 1767 Dihedral : 9.038 179.700 1464 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.65 % Allowed : 28.04 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1201 helix: 0.06 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 0.73 (0.34), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 535 TYR 0.019 0.002 TYR E 501 PHE 0.018 0.001 PHE B 476 TRP 0.010 0.001 TRP C 490 HIS 0.015 0.001 HIS E 530 Details of bonding type rmsd covalent geometry : bond 0.00412 (10132) covalent geometry : angle 0.83470 (13664) hydrogen bonds : bond 0.04670 ( 485) hydrogen bonds : angle 5.10608 ( 1327) Misc. bond : bond 0.00069 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 363 time to evaluate : 0.376 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: 0.6660 (OUTLIER) cc_final: 0.6374 (mm) REVERT: A 411 SER cc_start: 0.8073 (m) cc_final: 0.7794 (t) REVERT: A 450 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8409 (pt0) REVERT: A 454 ASP cc_start: 0.7490 (m-30) cc_final: 0.7266 (t0) REVERT: A 469 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 476 PHE cc_start: 0.8491 (m-10) cc_final: 0.8238 (m-10) REVERT: A 478 ASN cc_start: 0.8742 (t0) cc_final: 0.8360 (t0) REVERT: A 503 TYR cc_start: 0.8732 (t80) cc_final: 0.8358 (t80) REVERT: A 522 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7590 (mm-40) REVERT: A 529 ILE cc_start: 0.8277 (mt) cc_final: 0.7934 (tt) REVERT: B 413 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8587 (tmtt) REVERT: B 435 GLU cc_start: 0.9562 (tm-30) cc_final: 0.8990 (pp20) REVERT: B 438 VAL cc_start: 0.8453 (t) cc_final: 0.8241 (m) REVERT: B 479 TYR cc_start: 0.8336 (m-80) cc_final: 0.8002 (m-10) REVERT: B 490 TRP cc_start: 0.8178 (t-100) cc_final: 0.7792 (t-100) REVERT: C 457 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.5948 (mmm) REVERT: C 461 ILE cc_start: 0.9020 (tt) cc_final: 0.8799 (tt) REVERT: C 474 LYS cc_start: 0.9116 (mttm) cc_final: 0.8913 (mttt) REVERT: C 479 TYR cc_start: 0.8318 (m-80) cc_final: 0.7670 (m-80) REVERT: C 520 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7937 (tm-30) REVERT: C 521 GLN cc_start: 0.8268 (pp30) cc_final: 0.7912 (pp30) REVERT: C 525 GLU cc_start: 0.8932 (mp0) cc_final: 0.8427 (mp0) REVERT: D 431 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8041 (tm-30) REVERT: D 447 THR cc_start: 0.8224 (p) cc_final: 0.7521 (p) REVERT: D 449 GLU cc_start: 0.8820 (pp20) cc_final: 0.8181 (pp20) REVERT: D 454 ASP cc_start: 0.7719 (t0) cc_final: 0.7446 (t0) REVERT: D 472 GLU cc_start: 0.8434 (tp30) cc_final: 0.8065 (tp30) REVERT: D 476 PHE cc_start: 0.8730 (m-80) cc_final: 0.8159 (m-10) REVERT: D 497 ARG cc_start: 0.8524 (mtm110) cc_final: 0.8138 (ptp-170) REVERT: D 517 ARG cc_start: 0.9319 (mmm-85) cc_final: 0.9094 (mmm160) REVERT: D 522 GLN cc_start: 0.8663 (mt0) cc_final: 0.8371 (mm-40) REVERT: D 525 GLU cc_start: 0.9192 (mp0) cc_final: 0.8915 (mp0) REVERT: E 413 LYS cc_start: 0.9018 (tppp) cc_final: 0.8579 (tppp) REVERT: E 435 GLU cc_start: 0.9571 (tm-30) cc_final: 0.9123 (pp20) REVERT: F 426 PHE cc_start: 0.6381 (m-80) cc_final: 0.6172 (m-10) REVERT: F 479 TYR cc_start: 0.8034 (m-80) cc_final: 0.7603 (m-80) REVERT: F 524 LEU cc_start: 0.8304 (tt) cc_final: 0.7550 (pp) REVERT: G 468 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8102 (ttp80) REVERT: G 497 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8418 (ptp90) REVERT: G 503 TYR cc_start: 0.8687 (t80) cc_final: 0.8384 (t80) REVERT: G 511 ASP cc_start: 0.8932 (m-30) cc_final: 0.8674 (m-30) REVERT: G 517 ARG cc_start: 0.9467 (tpt-90) cc_final: 0.9240 (tpt-90) REVERT: G 522 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7536 (mm-40) REVERT: H 418 GLN cc_start: 0.8761 (mm110) cc_final: 0.8504 (mm110) REVERT: H 522 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8031 (mm-40) REVERT: H 545 MET cc_start: 0.5551 (ptt) cc_final: 0.5209 (ptt) outliers start: 29 outliers final: 19 residues processed: 382 average time/residue: 0.1075 time to fit residues: 54.8714 Evaluate side-chains 382 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 360 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 495 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 530 HIS Chi-restraints excluded: chain H residue 533 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 422 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 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 = 0.4184 r_free = 0.4184 target = 0.129690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090797 restraints weight = 146862.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.098129 restraints weight = 39087.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.103507 restraints weight = 20194.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.107344 restraints weight = 12701.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110169 restraints weight = 8918.149| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10140 Z= 0.174 Angle : 0.854 14.411 13664 Z= 0.423 Chirality : 0.046 0.284 1484 Planarity : 0.005 0.041 1767 Dihedral : 8.938 179.864 1464 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.65 % Allowed : 30.05 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1201 helix: 0.00 (0.19), residues: 769 sheet: None (None), residues: 0 loop : 0.58 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 484 TYR 0.019 0.002 TYR E 429 PHE 0.017 0.001 PHE H 476 TRP 0.015 0.002 TRP A 420 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00409 (10132) covalent geometry : angle 0.85387 (13664) hydrogen bonds : bond 0.04613 ( 485) hydrogen bonds : angle 5.22559 ( 1327) Misc. bond : bond 0.00068 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 383 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.8047 (m) cc_final: 0.7772 (t) REVERT: A 450 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8874 (pt0) REVERT: A 454 ASP cc_start: 0.7284 (m-30) cc_final: 0.7070 (t0) REVERT: A 472 GLU cc_start: 0.8256 (tp30) cc_final: 0.7843 (tp30) REVERT: A 476 PHE cc_start: 0.8492 (m-10) cc_final: 0.8262 (m-10) REVERT: A 478 ASN cc_start: 0.8651 (t0) cc_final: 0.8273 (t0) REVERT: A 503 TYR cc_start: 0.8677 (t80) cc_final: 0.8352 (t80) REVERT: A 522 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7584 (mm-40) REVERT: A 525 GLU cc_start: 0.9092 (mp0) cc_final: 0.8660 (mp0) REVERT: B 413 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8533 (tmtt) REVERT: B 435 GLU cc_start: 0.9556 (tm-30) cc_final: 0.9152 (pp20) REVERT: B 479 TYR cc_start: 0.8367 (m-80) cc_final: 0.8154 (m-10) REVERT: B 490 TRP cc_start: 0.8194 (t-100) cc_final: 0.7809 (t-100) REVERT: B 520 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7677 (tm-30) REVERT: C 474 LYS cc_start: 0.9119 (mttm) cc_final: 0.8910 (mttt) REVERT: C 479 TYR cc_start: 0.8216 (m-80) cc_final: 0.7617 (m-80) REVERT: C 521 GLN cc_start: 0.8287 (pp30) cc_final: 0.8022 (pp30) REVERT: C 525 GLU cc_start: 0.8917 (mp0) cc_final: 0.8505 (mp0) REVERT: D 413 LYS cc_start: 0.9208 (tmtt) cc_final: 0.8958 (mmmm) REVERT: D 414 GLU cc_start: 0.9296 (mp0) cc_final: 0.8042 (mp0) REVERT: D 431 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8060 (tm-30) REVERT: D 472 GLU cc_start: 0.8446 (tp30) cc_final: 0.8131 (tp30) REVERT: D 476 PHE cc_start: 0.8721 (m-80) cc_final: 0.8257 (m-10) REVERT: D 520 GLU cc_start: 0.7702 (pm20) cc_final: 0.6294 (mm-30) REVERT: D 522 GLN cc_start: 0.8692 (mt0) cc_final: 0.8353 (mm-40) REVERT: D 525 GLU cc_start: 0.9194 (mp0) cc_final: 0.8890 (mp0) REVERT: E 413 LYS cc_start: 0.9029 (tppp) cc_final: 0.8588 (tppp) REVERT: E 414 GLU cc_start: 0.9076 (pm20) cc_final: 0.8611 (pm20) REVERT: F 414 GLU cc_start: 0.9196 (mp0) cc_final: 0.8476 (mm-30) REVERT: F 426 PHE cc_start: 0.6284 (m-80) cc_final: 0.5856 (m-10) REVERT: F 457 MET cc_start: 0.6773 (mtt) cc_final: 0.6046 (mtp) REVERT: F 479 TYR cc_start: 0.8025 (m-80) cc_final: 0.7632 (m-80) REVERT: G 468 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8144 (ttp80) REVERT: G 476 PHE cc_start: 0.8819 (m-10) cc_final: 0.8617 (m-10) REVERT: G 497 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8435 (ptp90) REVERT: G 522 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7543 (mm-40) REVERT: G 543 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8079 (mtm110) REVERT: H 486 ASN cc_start: 0.9353 (t0) cc_final: 0.9123 (t0) REVERT: H 525 GLU cc_start: 0.8903 (mp0) cc_final: 0.8648 (mp0) REVERT: H 545 MET cc_start: 0.5731 (ptt) cc_final: 0.5342 (ptt) outliers start: 29 outliers final: 23 residues processed: 398 average time/residue: 0.1082 time to fit residues: 57.7829 Evaluate side-chains 379 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 355 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 495 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG 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 461 ILE Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 530 HIS Chi-restraints excluded: chain H residue 533 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS F 534 HIS ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 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 = 0.4160 r_free = 0.4160 target = 0.128030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089309 restraints weight = 168217.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.096553 restraints weight = 41150.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.101867 restraints weight = 20999.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.105590 restraints weight = 13151.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.108467 restraints weight = 9265.200| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10140 Z= 0.180 Angle : 0.877 11.731 13664 Z= 0.439 Chirality : 0.047 0.217 1484 Planarity : 0.005 0.042 1767 Dihedral : 8.823 179.778 1462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.38 % Allowed : 29.50 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1201 helix: -0.14 (0.19), residues: 769 sheet: None (None), residues: 0 loop : 0.52 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 484 TYR 0.028 0.002 TYR D 429 PHE 0.013 0.001 PHE G 476 TRP 0.016 0.002 TRP A 420 HIS 0.008 0.001 HIS H 530 Details of bonding type rmsd covalent geometry : bond 0.00429 (10132) covalent geometry : angle 0.87667 (13664) hydrogen bonds : bond 0.04412 ( 485) hydrogen bonds : angle 5.31652 ( 1327) Misc. bond : bond 0.00068 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 364 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.8073 (m) cc_final: 0.7795 (t) REVERT: A 450 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8890 (pt0) REVERT: A 454 ASP cc_start: 0.7525 (m-30) cc_final: 0.7244 (t0) REVERT: A 472 GLU cc_start: 0.8284 (tp30) cc_final: 0.7829 (tp30) REVERT: A 476 PHE cc_start: 0.8535 (m-10) cc_final: 0.8263 (m-10) REVERT: A 478 ASN cc_start: 0.8722 (t0) cc_final: 0.8367 (t0) REVERT: A 503 TYR cc_start: 0.8748 (t80) cc_final: 0.8398 (t80) REVERT: A 522 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7895 (mm-40) REVERT: A 525 GLU cc_start: 0.9111 (mp0) cc_final: 0.8629 (mp0) REVERT: A 544 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8626 (mm-30) REVERT: B 413 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8647 (tppp) REVERT: B 479 TYR cc_start: 0.8393 (m-80) cc_final: 0.8183 (m-10) REVERT: B 489 ASP cc_start: 0.9078 (m-30) cc_final: 0.8751 (t0) REVERT: B 490 TRP cc_start: 0.8169 (t-100) cc_final: 0.7782 (t-100) REVERT: B 503 TYR cc_start: 0.8297 (t80) cc_final: 0.8008 (t80) REVERT: C 479 TYR cc_start: 0.8181 (m-80) cc_final: 0.7587 (m-80) REVERT: C 520 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7777 (tm-30) REVERT: C 525 GLU cc_start: 0.8915 (mp0) cc_final: 0.8346 (mp0) REVERT: D 413 LYS cc_start: 0.9189 (tmtt) cc_final: 0.8938 (mmmm) REVERT: D 414 GLU cc_start: 0.9303 (mp0) cc_final: 0.8057 (mp0) REVERT: D 431 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8014 (tm-30) REVERT: D 472 GLU cc_start: 0.8441 (tp30) cc_final: 0.8094 (tp30) REVERT: D 476 PHE cc_start: 0.8712 (m-80) cc_final: 0.8243 (m-10) REVERT: D 497 ARG cc_start: 0.8389 (ptp-110) cc_final: 0.8078 (ptp90) REVERT: D 522 GLN cc_start: 0.8756 (mt0) cc_final: 0.8451 (mm-40) REVERT: D 525 GLU cc_start: 0.9189 (mp0) cc_final: 0.8890 (mp0) REVERT: E 413 LYS cc_start: 0.9062 (tppp) cc_final: 0.8603 (tppp) REVERT: F 414 GLU cc_start: 0.9225 (mp0) cc_final: 0.8836 (mp0) REVERT: F 426 PHE cc_start: 0.6368 (m-80) cc_final: 0.5984 (m-10) REVERT: F 457 MET cc_start: 0.6964 (mtt) cc_final: 0.6238 (mtp) REVERT: F 479 TYR cc_start: 0.8073 (m-80) cc_final: 0.7668 (m-80) REVERT: F 522 GLN cc_start: 0.8675 (mt0) cc_final: 0.8193 (mm-40) REVERT: F 524 LEU cc_start: 0.8438 (tt) cc_final: 0.7669 (pp) REVERT: F 529 ILE cc_start: 0.7445 (mm) cc_final: 0.7034 (mm) REVERT: G 414 GLU cc_start: 0.9374 (mp0) cc_final: 0.8834 (mp0) REVERT: G 423 GLN cc_start: 0.9409 (tm-30) cc_final: 0.9123 (tm-30) REVERT: G 424 ILE cc_start: 0.8978 (pt) cc_final: 0.8591 (pt) REVERT: G 468 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8159 (ttp80) REVERT: G 497 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8447 (ptp90) REVERT: G 521 GLN cc_start: 0.9192 (tt0) cc_final: 0.8691 (pp30) REVERT: H 486 ASN cc_start: 0.9394 (t0) cc_final: 0.9150 (t0) REVERT: H 503 TYR cc_start: 0.8449 (t80) cc_final: 0.8145 (t80) REVERT: H 522 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8505 (mm-40) REVERT: H 545 MET cc_start: 0.5789 (ptt) cc_final: 0.5401 (ptt) outliers start: 37 outliers final: 31 residues processed: 384 average time/residue: 0.1057 time to fit residues: 54.4670 Evaluate side-chains 382 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 350 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 452 GLN Chi-restraints excluded: chain A residue 495 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 B residue 447 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 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 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 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 530 HIS Chi-restraints excluded: chain H residue 533 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 0.0980 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 59 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 17 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS G 436 GLN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 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 = 0.4178 r_free = 0.4178 target = 0.129138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.089961 restraints weight = 168369.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.097357 restraints weight = 41666.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.102748 restraints weight = 21318.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.106589 restraints weight = 13353.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109398 restraints weight = 9369.950| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10140 Z= 0.173 Angle : 0.908 12.679 13664 Z= 0.446 Chirality : 0.048 0.250 1484 Planarity : 0.005 0.051 1767 Dihedral : 8.696 179.843 1462 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.74 % Allowed : 30.68 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.25), residues: 1201 helix: -0.22 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.49 (0.34), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 517 TYR 0.020 0.002 TYR E 501 PHE 0.022 0.001 PHE B 476 TRP 0.016 0.002 TRP D 490 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00414 (10132) covalent geometry : angle 0.90828 (13664) hydrogen bonds : bond 0.04333 ( 485) hydrogen bonds : angle 5.37075 ( 1327) Misc. bond : bond 0.00052 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 376 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7997 (m) cc_final: 0.7739 (t) REVERT: A 450 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8981 (pt0) REVERT: A 454 ASP cc_start: 0.7415 (m-30) cc_final: 0.7095 (t0) REVERT: A 478 ASN cc_start: 0.8762 (t0) cc_final: 0.8395 (t0) REVERT: A 503 TYR cc_start: 0.8720 (t80) cc_final: 0.8352 (t80) REVERT: A 522 GLN cc_start: 0.8601 (mm-40) cc_final: 0.7663 (mm-40) REVERT: A 544 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8612 (mm-30) REVERT: B 435 GLU cc_start: 0.9504 (tm-30) cc_final: 0.9102 (pp20) REVERT: B 449 GLU cc_start: 0.8834 (tp30) cc_final: 0.8619 (tp30) REVERT: B 489 ASP cc_start: 0.9128 (m-30) cc_final: 0.8876 (t0) REVERT: B 490 TRP cc_start: 0.8153 (t-100) cc_final: 0.7762 (t-100) REVERT: B 521 GLN cc_start: 0.8440 (tp40) cc_final: 0.8239 (pp30) REVERT: B 522 GLN cc_start: 0.8650 (mt0) cc_final: 0.8420 (tp-100) REVERT: B 530 HIS cc_start: 0.8310 (m90) cc_final: 0.8084 (m-70) REVERT: C 479 TYR cc_start: 0.8133 (m-80) cc_final: 0.7590 (m-80) REVERT: C 520 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 525 GLU cc_start: 0.8866 (mp0) cc_final: 0.8311 (mp0) REVERT: D 413 LYS cc_start: 0.9185 (tmtt) cc_final: 0.8955 (mmmm) REVERT: D 414 GLU cc_start: 0.9283 (mp0) cc_final: 0.8050 (mp0) REVERT: D 431 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7991 (tm-30) REVERT: D 472 GLU cc_start: 0.8453 (tp30) cc_final: 0.8102 (tm-30) REVERT: D 476 PHE cc_start: 0.8704 (m-80) cc_final: 0.8447 (m-10) REVERT: D 497 ARG cc_start: 0.8369 (ptp-110) cc_final: 0.8077 (ptp90) REVERT: D 520 GLU cc_start: 0.7830 (pm20) cc_final: 0.6467 (mm-30) REVERT: D 522 GLN cc_start: 0.8731 (mt0) cc_final: 0.8355 (mm-40) REVERT: D 525 GLU cc_start: 0.9182 (mp0) cc_final: 0.8871 (mp0) REVERT: E 413 LYS cc_start: 0.9032 (tppp) cc_final: 0.8569 (tppp) REVERT: E 457 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6361 (mmm) REVERT: E 497 ARG cc_start: 0.9095 (mtm180) cc_final: 0.8633 (ptp90) REVERT: E 543 ARG cc_start: 0.9017 (mmt90) cc_final: 0.8261 (mtm110) REVERT: E 544 GLU cc_start: 0.8026 (mp0) cc_final: 0.7735 (mp0) REVERT: F 414 GLU cc_start: 0.9242 (mp0) cc_final: 0.8839 (mp0) REVERT: F 416 GLU cc_start: 0.8703 (mp0) cc_final: 0.8472 (pm20) REVERT: F 426 PHE cc_start: 0.6319 (m-80) cc_final: 0.5986 (m-10) REVERT: F 457 MET cc_start: 0.7205 (mtt) cc_final: 0.6542 (mtp) REVERT: F 479 TYR cc_start: 0.8073 (m-80) cc_final: 0.7638 (m-80) REVERT: F 524 LEU cc_start: 0.8412 (tt) cc_final: 0.7642 (pp) REVERT: F 529 ILE cc_start: 0.7617 (mm) cc_final: 0.7286 (mm) REVERT: G 414 GLU cc_start: 0.9388 (mp0) cc_final: 0.8861 (mp0) REVERT: G 423 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9150 (tm-30) REVERT: G 424 ILE cc_start: 0.9006 (pt) cc_final: 0.8623 (pt) REVERT: G 431 GLU cc_start: 0.8782 (tp30) cc_final: 0.8526 (tm-30) REVERT: G 468 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8252 (ttp80) REVERT: G 497 ARG cc_start: 0.8823 (mtm-85) cc_final: 0.8553 (ptp90) REVERT: G 521 GLN cc_start: 0.9286 (tt0) cc_final: 0.8831 (pp30) REVERT: H 413 LYS cc_start: 0.9172 (tppp) cc_final: 0.8630 (tmtt) REVERT: H 418 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8588 (mm110) REVERT: H 454 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7202 (t0) REVERT: H 486 ASN cc_start: 0.9383 (t0) cc_final: 0.9089 (t0) REVERT: H 522 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8451 (mm-40) REVERT: H 545 MET cc_start: 0.5722 (ptt) cc_final: 0.5483 (ptt) outliers start: 30 outliers final: 21 residues processed: 392 average time/residue: 0.1102 time to fit residues: 57.7453 Evaluate side-chains 388 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 364 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 523 LEU 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 452 GLN Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 530 HIS Chi-restraints excluded: chain H residue 533 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 73 optimal weight: 0.0050 chunk 71 optimal weight: 0.0370 chunk 48 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9874 ------------------------------------------------------------------------------- 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 436 GLN A 452 GLN ** B 418 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 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 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 = 0.4176 r_free = 0.4176 target = 0.128827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.090043 restraints weight = 157243.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.097301 restraints weight = 40830.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.102589 restraints weight = 21092.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106407 restraints weight = 13272.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109160 restraints weight = 9336.516| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10140 Z= 0.175 Angle : 0.921 12.924 13664 Z= 0.453 Chirality : 0.048 0.243 1484 Planarity : 0.005 0.051 1767 Dihedral : 8.583 179.861 1460 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.38 % Allowed : 30.96 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1201 helix: -0.21 (0.19), residues: 767 sheet: None (None), residues: 0 loop : 0.49 (0.35), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 484 TYR 0.019 0.002 TYR E 501 PHE 0.010 0.001 PHE G 476 TRP 0.015 0.001 TRP C 490 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00419 (10132) covalent geometry : angle 0.92101 (13664) hydrogen bonds : bond 0.04207 ( 485) hydrogen bonds : angle 5.35682 ( 1327) Misc. bond : bond 0.00052 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 370 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7979 (m) cc_final: 0.7726 (t) REVERT: A 450 GLU cc_start: 0.9228 (mt-10) cc_final: 0.9011 (pt0) REVERT: A 454 ASP cc_start: 0.7198 (m-30) cc_final: 0.6903 (t0) REVERT: A 472 GLU cc_start: 0.8226 (tp30) cc_final: 0.7968 (tp30) REVERT: A 478 ASN cc_start: 0.8708 (t0) cc_final: 0.8363 (t0) REVERT: A 503 TYR cc_start: 0.8719 (t80) cc_final: 0.8418 (t80) REVERT: A 525 GLU cc_start: 0.9117 (mp0) cc_final: 0.8698 (mp0) REVERT: A 544 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8617 (mm-30) REVERT: B 435 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9082 (pp20) REVERT: B 479 TYR cc_start: 0.7616 (m-10) cc_final: 0.7364 (m-10) REVERT: B 489 ASP cc_start: 0.9120 (m-30) cc_final: 0.8812 (t0) REVERT: B 490 TRP cc_start: 0.8159 (t-100) cc_final: 0.7770 (t-100) REVERT: B 521 GLN cc_start: 0.8468 (tp40) cc_final: 0.8248 (pp30) REVERT: C 474 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8954 (mttp) REVERT: C 479 TYR cc_start: 0.8085 (m-80) cc_final: 0.7563 (m-80) REVERT: C 520 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 525 GLU cc_start: 0.8821 (mp0) cc_final: 0.8247 (mp0) REVERT: D 431 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7949 (tm-30) REVERT: D 449 GLU cc_start: 0.8923 (pm20) cc_final: 0.8660 (pm20) REVERT: D 472 GLU cc_start: 0.8456 (tp30) cc_final: 0.8046 (tm-30) REVERT: D 473 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8566 (mt) REVERT: D 476 PHE cc_start: 0.8668 (m-80) cc_final: 0.8399 (m-10) REVERT: D 520 GLU cc_start: 0.7972 (pm20) cc_final: 0.6725 (mm-30) REVERT: D 522 GLN cc_start: 0.8720 (mt0) cc_final: 0.8402 (mt0) REVERT: D 525 GLU cc_start: 0.9145 (mp0) cc_final: 0.8821 (mp0) REVERT: E 413 LYS cc_start: 0.9033 (tppp) cc_final: 0.8575 (tppp) REVERT: E 497 ARG cc_start: 0.9116 (mtm180) cc_final: 0.8684 (ptp90) REVERT: E 503 TYR cc_start: 0.8283 (t80) cc_final: 0.8080 (t80) REVERT: E 543 ARG cc_start: 0.9004 (mmt90) cc_final: 0.8185 (mtm110) REVERT: F 416 GLU cc_start: 0.8714 (mp0) cc_final: 0.8357 (pm20) REVERT: F 426 PHE cc_start: 0.6347 (m-80) cc_final: 0.6036 (m-10) REVERT: F 457 MET cc_start: 0.7308 (mtt) cc_final: 0.6662 (mtp) REVERT: F 479 TYR cc_start: 0.8091 (m-80) cc_final: 0.7646 (m-80) REVERT: F 522 GLN cc_start: 0.8669 (mt0) cc_final: 0.8191 (mm-40) REVERT: F 524 LEU cc_start: 0.8412 (tt) cc_final: 0.7889 (pp) REVERT: F 529 ILE cc_start: 0.7744 (mm) cc_final: 0.7399 (mm) REVERT: G 413 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8649 (tmtt) REVERT: G 414 GLU cc_start: 0.9393 (mp0) cc_final: 0.8758 (mp0) REVERT: G 423 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9160 (tm-30) REVERT: G 424 ILE cc_start: 0.9010 (pt) cc_final: 0.8629 (pt) REVERT: G 468 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8285 (ttp80) REVERT: G 497 ARG cc_start: 0.8841 (mtm-85) cc_final: 0.8555 (ptp90) REVERT: G 520 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7383 (tm-30) REVERT: G 522 GLN cc_start: 0.8919 (tp40) cc_final: 0.8684 (tp40) REVERT: H 413 LYS cc_start: 0.9163 (tppp) cc_final: 0.8663 (tmtt) REVERT: H 418 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8597 (mm110) REVERT: H 454 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7262 (t0) REVERT: H 486 ASN cc_start: 0.9372 (t0) cc_final: 0.9033 (t0) REVERT: H 520 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7971 (tm-30) REVERT: H 522 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8176 (tp-100) REVERT: H 545 MET cc_start: 0.5760 (ptt) cc_final: 0.5551 (ptt) outliers start: 26 outliers final: 19 residues processed: 383 average time/residue: 0.0960 time to fit residues: 49.9927 Evaluate side-chains 368 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 346 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 530 HIS Chi-restraints excluded: chain H residue 533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 111 optimal weight: 0.1980 chunk 69 optimal weight: 0.1980 chunk 67 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN H 530 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.128778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.089872 restraints weight = 166993.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.097073 restraints weight = 42015.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.102414 restraints weight = 21625.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.106186 restraints weight = 13599.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109074 restraints weight = 9546.884| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.3895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.7368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10140 Z= 0.178 Angle : 0.937 13.403 13664 Z= 0.462 Chirality : 0.048 0.244 1484 Planarity : 0.005 0.062 1767 Dihedral : 8.528 179.872 1460 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.92 % Allowed : 31.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1201 helix: -0.21 (0.19), residues: 766 sheet: None (None), residues: 0 loop : 0.45 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 484 TYR 0.020 0.002 TYR B 503 PHE 0.018 0.001 PHE A 476 TRP 0.015 0.002 TRP C 490 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00429 (10132) covalent geometry : angle 0.93738 (13664) hydrogen bonds : bond 0.04216 ( 485) hydrogen bonds : angle 5.33257 ( 1327) Misc. bond : bond 0.00048 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 359 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7969 (m) cc_final: 0.7709 (t) REVERT: A 444 LEU cc_start: 0.8603 (mp) cc_final: 0.8317 (mp) REVERT: A 450 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8806 (pt0) REVERT: A 478 ASN cc_start: 0.8719 (t0) cc_final: 0.8389 (t0) REVERT: A 503 TYR cc_start: 0.8740 (t80) cc_final: 0.8406 (t80) REVERT: A 520 GLU cc_start: 0.8858 (pm20) cc_final: 0.8657 (pm20) REVERT: A 525 GLU cc_start: 0.9108 (mp0) cc_final: 0.8698 (mp0) REVERT: A 544 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8581 (mm-30) REVERT: B 489 ASP cc_start: 0.9153 (m-30) cc_final: 0.8898 (t0) REVERT: B 490 TRP cc_start: 0.8162 (t-100) cc_final: 0.7830 (t-100) REVERT: B 503 TYR cc_start: 0.8172 (t80) cc_final: 0.7662 (t80) REVERT: C 479 TYR cc_start: 0.8086 (m-80) cc_final: 0.7655 (m-80) REVERT: C 520 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7751 (tm-30) REVERT: C 521 GLN cc_start: 0.8361 (pp30) cc_final: 0.7788 (pp30) REVERT: C 525 GLU cc_start: 0.8824 (mp0) cc_final: 0.8231 (mp0) REVERT: C 533 VAL cc_start: 0.9274 (p) cc_final: 0.9012 (m) REVERT: D 411 SER cc_start: 0.8092 (m) cc_final: 0.7655 (t) REVERT: D 413 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8866 (mmmm) REVERT: D 414 GLU cc_start: 0.9087 (mp0) cc_final: 0.8257 (mp0) REVERT: D 416 GLU cc_start: 0.9371 (pm20) cc_final: 0.9115 (pm20) REVERT: D 431 GLU cc_start: 0.8554 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 472 GLU cc_start: 0.8445 (tp30) cc_final: 0.8025 (tm-30) REVERT: D 473 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8577 (mt) REVERT: D 476 PHE cc_start: 0.8663 (m-80) cc_final: 0.8386 (m-10) REVERT: D 520 GLU cc_start: 0.7982 (pm20) cc_final: 0.6653 (mm-30) REVERT: D 522 GLN cc_start: 0.8743 (mt0) cc_final: 0.8357 (mm-40) REVERT: D 525 GLU cc_start: 0.9151 (mp0) cc_final: 0.8817 (mp0) REVERT: E 413 LYS cc_start: 0.9044 (tppp) cc_final: 0.8577 (tppp) REVERT: E 449 GLU cc_start: 0.8814 (tp30) cc_final: 0.8570 (tp30) REVERT: E 457 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6458 (mmt) REVERT: E 458 LYS cc_start: 0.9009 (tptt) cc_final: 0.8668 (tppt) REVERT: E 497 ARG cc_start: 0.9117 (mtm180) cc_final: 0.8692 (ptp90) REVERT: F 414 GLU cc_start: 0.9371 (mp0) cc_final: 0.8726 (mp0) REVERT: F 416 GLU cc_start: 0.8719 (mp0) cc_final: 0.8480 (pm20) REVERT: F 426 PHE cc_start: 0.6287 (m-80) cc_final: 0.5989 (m-10) REVERT: F 457 MET cc_start: 0.7276 (mtt) cc_final: 0.6633 (mtp) REVERT: F 479 TYR cc_start: 0.8045 (m-80) cc_final: 0.7629 (m-80) REVERT: F 522 GLN cc_start: 0.8705 (mt0) cc_final: 0.8203 (mm-40) REVERT: F 524 LEU cc_start: 0.8409 (tt) cc_final: 0.7874 (pp) REVERT: F 529 ILE cc_start: 0.7387 (mm) cc_final: 0.7001 (mm) REVERT: G 414 GLU cc_start: 0.9392 (mp0) cc_final: 0.8801 (mp0) REVERT: G 423 GLN cc_start: 0.9403 (tm-30) cc_final: 0.9165 (tm-30) REVERT: G 424 ILE cc_start: 0.9102 (pt) cc_final: 0.8741 (pt) REVERT: G 431 GLU cc_start: 0.8813 (tp30) cc_final: 0.8536 (tm-30) REVERT: G 468 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8310 (ttp80) REVERT: G 497 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8557 (ptp90) REVERT: G 522 GLN cc_start: 0.8975 (tp40) cc_final: 0.8604 (tp40) REVERT: H 451 LEU cc_start: 0.9112 (tp) cc_final: 0.8884 (tp) REVERT: H 454 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7243 (t0) REVERT: H 486 ASN cc_start: 0.9380 (t0) cc_final: 0.9071 (t0) REVERT: H 503 TYR cc_start: 0.8598 (t80) cc_final: 0.8382 (t80) REVERT: H 522 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8151 (tp-100) outliers start: 21 outliers final: 17 residues processed: 369 average time/residue: 0.0941 time to fit residues: 47.4519 Evaluate side-chains 380 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 359 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 530 HIS Chi-restraints excluded: chain H residue 533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.0170 chunk 75 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2624 ------------------------------------------------------------------------------- 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 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN H 530 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.128104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.089346 restraints weight = 161921.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.096459 restraints weight = 41679.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.101713 restraints weight = 21625.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.105432 restraints weight = 13681.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.108334 restraints weight = 9639.447| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10140 Z= 0.178 Angle : 0.936 14.315 13664 Z= 0.462 Chirality : 0.048 0.236 1484 Planarity : 0.005 0.069 1767 Dihedral : 8.506 179.860 1460 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.74 % Allowed : 32.15 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1201 helix: -0.20 (0.19), residues: 765 sheet: None (None), residues: 0 loop : 0.46 (0.35), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 484 TYR 0.049 0.003 TYR B 501 PHE 0.010 0.001 PHE C 466 TRP 0.014 0.001 TRP C 490 HIS 0.009 0.001 HIS H 530 Details of bonding type rmsd covalent geometry : bond 0.00434 (10132) covalent geometry : angle 0.93614 (13664) hydrogen bonds : bond 0.04140 ( 485) hydrogen bonds : angle 5.29148 ( 1327) Misc. bond : bond 0.00052 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.96 seconds wall clock time: 40 minutes 16.85 seconds (2416.85 seconds total)