Starting phenix.real_space_refine on Mon Jan 20 19:23:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3r_38896/01_2025/8y3r_38896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3r_38896/01_2025/8y3r_38896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3r_38896/01_2025/8y3r_38896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3r_38896/01_2025/8y3r_38896.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3r_38896/01_2025/8y3r_38896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3r_38896/01_2025/8y3r_38896.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.127 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 69 5.16 5 C 10056 2.51 5 N 2697 2.21 5 O 2913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15735 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3499 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 33, 'TRANS': 403} Chain breaks: 3 Chain: "B" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 808 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3499 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 33, 'TRANS': 403} Chain breaks: 3 Chain: "E" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 808 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "D" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3499 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 33, 'TRANS': 403} Chain breaks: 3 Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 808 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Time building chain proxies: 9.51, per 1000 atoms: 0.60 Number of scatterers: 15735 At special positions: 0 Unit cell: (113.42, 110.21, 135.89, 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 69 16.00 O 2913 8.00 N 2697 7.00 C 10056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 1.9 seconds 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 39 sheets defined 9.2% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.714A pdb=" N VAL A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.695A pdb=" N ALA A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.720A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 367' Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'C' and resid 205 through 215 removed outlier: 3.523A pdb=" N PHE C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 228 removed outlier: 3.825A pdb=" N VAL C 228 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.704A pdb=" N ALA C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.731A pdb=" N LEU C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 367' Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 560 through 566 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 221 through 228 removed outlier: 3.758A pdb=" N VAL D 228 " --> pdb=" O TYR D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 removed outlier: 3.698A pdb=" N ALA D 344 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.828A pdb=" N LEU D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 367' Processing helix chain 'D' and resid 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 554 through 560 removed outlier: 4.042A pdb=" N CYS D 558 " --> pdb=" O PRO D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 566 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'H' and resid 30 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 92 removed outlier: 3.822A pdb=" N ASP A 194 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 190 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.718A pdb=" N PHE A 100 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 417 " --> pdb=" O PHE A 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 109 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.773A pdb=" N TYR A 173 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 158 removed outlier: 6.277A pdb=" N SER A 387 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER A 521 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 523 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 391 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 522 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA7, first strand: chain 'A' and resid 234 through 246 removed outlier: 5.785A pdb=" N ASN A 309 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG A 307 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A 242 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP A 305 " --> pdb=" O LEU A 242 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 305 through 314 current: chain 'A' and resid 528 through 533 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 528 through 533 current: chain 'C' and resid 305 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 305 through 314 current: chain 'C' and resid 528 through 533 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 528 through 533 current: chain 'D' and resid 305 through 314 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 305 through 314 current: chain 'D' and resid 528 through 533 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 582 Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 554 removed outlier: 4.981A pdb=" N ASP A 551 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 542 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 541 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.941A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 4.409A pdb=" N MET L 10 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS L 90 " --> pdb=" O GLY L 102 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY L 104 " --> pdb=" O TYR L 88 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR L 88 " --> pdb=" O GLY L 104 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE L 89 " --> pdb=" O PHE L 38 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE L 38 " --> pdb=" O PHE L 89 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 92 removed outlier: 3.809A pdb=" N ASP C 194 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN C 190 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 100 through 101 removed outlier: 4.729A pdb=" N PHE C 100 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 417 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 105 through 109 Processing sheet with id=AB8, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.671A pdb=" N TYR C 173 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 153 through 158 Processing sheet with id=AC1, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AC2, first strand: chain 'C' and resid 579 through 582 Processing sheet with id=AC3, first strand: chain 'C' and resid 501 through 503 removed outlier: 3.982A pdb=" N ILE C 522 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 550 through 554 removed outlier: 4.891A pdb=" N ASP C 551 " --> pdb=" O VAL C 542 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 542 " --> pdb=" O ASP C 551 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.896A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 9 through 12 removed outlier: 4.382A pdb=" N MET G 10 " --> pdb=" O HIS G 106 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS G 90 " --> pdb=" O GLY G 102 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY G 104 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR G 88 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE G 89 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE G 38 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 89 through 92 removed outlier: 3.807A pdb=" N ASP D 194 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN D 190 " --> pdb=" O LYS D 360 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 100 through 101 removed outlier: 4.731A pdb=" N PHE D 100 " --> pdb=" O LEU D 417 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU D 417 " --> pdb=" O PHE D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 105 through 109 Processing sheet with id=AD3, first strand: chain 'D' and resid 117 through 118 removed outlier: 3.754A pdb=" N TYR D 173 " --> pdb=" O GLN D 118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 154 through 158 Processing sheet with id=AD5, first strand: chain 'D' and resid 176 through 179 Processing sheet with id=AD6, first strand: chain 'D' and resid 580 through 582 Processing sheet with id=AD7, first strand: chain 'D' and resid 501 through 503 removed outlier: 3.875A pdb=" N ILE D 522 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 550 through 553 removed outlier: 4.980A pdb=" N ASP D 551 " --> pdb=" O VAL D 542 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 542 " --> pdb=" O ASP D 551 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 541 " --> pdb=" O SER D 609 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.915A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.433A pdb=" N MET H 10 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N CYS H 90 " --> pdb=" O GLY H 102 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY H 104 " --> pdb=" O TYR H 88 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR H 88 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE H 89 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE H 38 " --> pdb=" O PHE H 89 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 918 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: 6.04 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4903 1.34 - 1.46: 2958 1.46 - 1.58: 8219 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 16179 Sorted by residual: bond pdb=" N TYR H 34 " pdb=" CA TYR H 34 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.40e-03 1.83e+04 2.09e+01 bond pdb=" N LEU A 515 " pdb=" CA LEU A 515 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.34e+01 bond pdb=" N ARG C 385 " pdb=" CA ARG C 385 " ideal model delta sigma weight residual 1.461 1.491 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N ARG A 385 " pdb=" CA ARG A 385 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 1.00e+01 bond pdb=" N ASP D 512 " pdb=" CA ASP D 512 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.24e-02 6.50e+03 9.47e+00 ... (remaining 16174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 21716 2.32 - 4.65: 311 4.65 - 6.97: 27 6.97 - 9.29: 0 9.29 - 11.62: 2 Bond angle restraints: 22056 Sorted by residual: angle pdb=" N ASP D 512 " pdb=" CA ASP D 512 " pdb=" C ASP D 512 " ideal model delta sigma weight residual 112.13 105.66 6.47 1.37e+00 5.33e-01 2.23e+01 angle pdb=" CA GLY C 384 " pdb=" C GLY C 384 " pdb=" O GLY C 384 " ideal model delta sigma weight residual 122.78 117.83 4.95 1.20e+00 6.94e-01 1.70e+01 angle pdb=" CA GLY A 384 " pdb=" C GLY A 384 " pdb=" O GLY A 384 " ideal model delta sigma weight residual 122.78 117.87 4.91 1.20e+00 6.94e-01 1.67e+01 angle pdb=" CA THR C 513 " pdb=" C THR C 513 " pdb=" O THR C 513 " ideal model delta sigma weight residual 121.54 117.52 4.02 1.16e+00 7.43e-01 1.20e+01 angle pdb=" N ILE H 96 " pdb=" CA ILE H 96 " pdb=" C ILE H 96 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.19e+01 ... (remaining 22051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8563 18.00 - 35.99: 768 35.99 - 53.99: 99 53.99 - 71.98: 22 71.98 - 89.98: 13 Dihedral angle restraints: 9465 sinusoidal: 3735 harmonic: 5730 Sorted by residual: dihedral pdb=" CB CYS B 101 " pdb=" SG CYS B 101 " pdb=" SG CYS B 105 " pdb=" CB CYS B 105 " ideal model delta sinusoidal sigma weight residual 93.00 54.56 38.44 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CA GLU C 202 " pdb=" C GLU C 202 " pdb=" N TYR C 203 " pdb=" CA TYR C 203 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLU A 202 " pdb=" C GLU A 202 " pdb=" N TYR A 203 " pdb=" CA TYR A 203 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 9462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1740 0.042 - 0.084: 388 0.084 - 0.127: 236 0.127 - 0.169: 31 0.169 - 0.211: 5 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CA LEU A 515 " pdb=" N LEU A 515 " pdb=" C LEU A 515 " pdb=" CB LEU A 515 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LEU D 515 " pdb=" N LEU D 515 " pdb=" C LEU D 515 " pdb=" CB LEU D 515 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU C 515 " pdb=" N LEU C 515 " pdb=" C LEU C 515 " pdb=" CB LEU C 515 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2397 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 7 " -0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO H 8 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO H 8 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 8 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 324 " 0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO D 325 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO D 325 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 325 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 324 " -0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO C 325 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " -0.052 5.00e-02 4.00e+02 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 804 2.73 - 3.27: 15046 3.27 - 3.82: 24282 3.82 - 4.36: 28727 4.36 - 4.90: 50877 Nonbonded interactions: 119736 Sorted by model distance: nonbonded pdb=" OH TYR H 93 " pdb=" O ILE H 96 " model vdw 2.188 3.040 nonbonded pdb=" OE2 GLU H 7 " pdb=" OG1 THR H 21 " model vdw 2.239 3.040 nonbonded pdb=" OD2 ASP C 103 " pdb=" NZ LYS C 332 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR A 85 " pdb=" OD1 ASN A 88 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR D 85 " pdb=" OD1 ASN D 88 " model vdw 2.248 3.040 ... (remaining 119731 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.180 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16179 Z= 0.220 Angle : 0.617 11.615 22056 Z= 0.349 Chirality : 0.047 0.211 2400 Planarity : 0.006 0.100 2862 Dihedral : 13.770 89.980 5784 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.33 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 1965 helix: -0.80 (0.60), residues: 72 sheet: -1.08 (0.18), residues: 807 loop : -0.47 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 330 HIS 0.003 0.001 HIS D 107 PHE 0.013 0.001 PHE C 557 TYR 0.037 0.001 TYR D 203 ARG 0.004 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6269 (mtmm) cc_final: 0.5905 (mtpp) REVERT: A 502 HIS cc_start: 0.7005 (m-70) cc_final: 0.5083 (t-90) REVERT: B 7 SER cc_start: 0.8170 (t) cc_final: 0.7735 (p) REVERT: L 30 THR cc_start: 0.8321 (p) cc_final: 0.7935 (t) REVERT: L 81 GLN cc_start: 0.7508 (mp-120) cc_final: 0.6870 (mt0) REVERT: C 209 THR cc_start: 0.7213 (m) cc_final: 0.6538 (p) REVERT: C 581 MET cc_start: 0.6300 (ttt) cc_final: 0.5896 (ttt) REVERT: G 81 GLN cc_start: 0.7643 (mp-120) cc_final: 0.7271 (mt0) REVERT: G 91 THR cc_start: 0.8116 (t) cc_final: 0.7850 (t) REVERT: D 209 THR cc_start: 0.7404 (m) cc_final: 0.6755 (p) REVERT: D 572 LYS cc_start: 0.7267 (tttt) cc_final: 0.7029 (ttmt) REVERT: F 7 SER cc_start: 0.8230 (t) cc_final: 0.7661 (p) REVERT: H 81 GLN cc_start: 0.7423 (mp-120) cc_final: 0.7090 (mt0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2926 time to fit residues: 139.3712 Evaluate side-chains 222 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 0.0000 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 484 HIS L 44 GLN L 106 HIS C 102 HIS C 484 HIS C 502 HIS G 33 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS D 102 HIS ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS D 484 HIS D 502 HIS H 33 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.203113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.167680 restraints weight = 180623.619| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 8.88 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16179 Z= 0.189 Angle : 0.589 6.976 22056 Z= 0.307 Chirality : 0.048 0.246 2400 Planarity : 0.005 0.074 2862 Dihedral : 4.447 18.768 2169 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.20 % Allowed : 9.45 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1965 helix: -0.64 (0.56), residues: 75 sheet: -0.95 (0.18), residues: 798 loop : -0.39 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 100 HIS 0.005 0.001 HIS D 482 PHE 0.011 0.001 PHE E 29 TYR 0.019 0.001 TYR H 51 ARG 0.005 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.8304 (m) cc_final: 0.7690 (p) REVERT: A 502 HIS cc_start: 0.7173 (m-70) cc_final: 0.5805 (t-90) REVERT: L 30 THR cc_start: 0.8445 (p) cc_final: 0.8225 (t) REVERT: L 44 GLN cc_start: 0.7579 (mm110) cc_final: 0.7194 (mp10) REVERT: L 81 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7280 (mt0) REVERT: C 209 THR cc_start: 0.8184 (m) cc_final: 0.7676 (p) REVERT: C 221 MET cc_start: 0.7462 (tpt) cc_final: 0.7016 (tpt) REVERT: G 81 GLN cc_start: 0.7915 (mp-120) cc_final: 0.7513 (mt0) REVERT: D 502 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.7104 (m170) REVERT: F 7 SER cc_start: 0.8226 (t) cc_final: 0.7885 (p) REVERT: F 53 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8277 (mtmm) REVERT: H 106 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6533 (t-170) outliers start: 38 outliers final: 24 residues processed: 251 average time/residue: 0.2636 time to fit residues: 101.2262 Evaluate side-chains 235 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 390 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.199682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.163914 restraints weight = 180059.108| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 9.14 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16179 Z= 0.193 Angle : 0.558 7.205 22056 Z= 0.289 Chirality : 0.046 0.167 2400 Planarity : 0.004 0.066 2862 Dihedral : 4.375 18.123 2169 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.07 % Allowed : 12.41 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1965 helix: 0.44 (0.60), residues: 75 sheet: -0.84 (0.18), residues: 834 loop : -0.09 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 100 HIS 0.005 0.001 HIS D 502 PHE 0.010 0.001 PHE C 557 TYR 0.023 0.002 TYR H 51 ARG 0.004 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6907 (mp0) REVERT: A 502 HIS cc_start: 0.7319 (m-70) cc_final: 0.6052 (t-90) REVERT: A 532 ILE cc_start: 0.8532 (mp) cc_final: 0.8152 (mt) REVERT: L 30 THR cc_start: 0.8526 (p) cc_final: 0.8238 (t) REVERT: L 44 GLN cc_start: 0.7723 (mm110) cc_final: 0.7353 (mp10) REVERT: L 81 GLN cc_start: 0.7690 (mp-120) cc_final: 0.7349 (mm-40) REVERT: C 209 THR cc_start: 0.8469 (m) cc_final: 0.7912 (p) REVERT: C 221 MET cc_start: 0.7432 (tpt) cc_final: 0.6907 (tpt) REVERT: G 81 GLN cc_start: 0.7744 (mp-120) cc_final: 0.7294 (mt0) REVERT: D 88 ASN cc_start: 0.8779 (m110) cc_final: 0.8555 (m-40) REVERT: D 502 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7248 (m170) REVERT: F 7 SER cc_start: 0.8255 (t) cc_final: 0.8000 (p) REVERT: F 53 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8223 (mtmm) outliers start: 53 outliers final: 39 residues processed: 238 average time/residue: 0.2623 time to fit residues: 96.2209 Evaluate side-chains 242 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 188 optimal weight: 0.0020 chunk 93 optimal weight: 0.9980 chunk 168 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 390 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS D 390 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.199293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.164021 restraints weight = 181719.222| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 8.96 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16179 Z= 0.160 Angle : 0.530 7.106 22056 Z= 0.274 Chirality : 0.045 0.164 2400 Planarity : 0.004 0.060 2862 Dihedral : 4.271 18.224 2169 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.77 % Favored : 96.08 % Rotamer: Outliers : 3.65 % Allowed : 12.70 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1965 helix: 0.73 (0.59), residues: 75 sheet: -0.76 (0.18), residues: 816 loop : -0.11 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 330 HIS 0.012 0.001 HIS D 502 PHE 0.009 0.001 PHE E 29 TYR 0.021 0.001 TYR D 178 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6793 (mp0) REVERT: A 502 HIS cc_start: 0.7327 (m-70) cc_final: 0.6123 (t-90) REVERT: A 532 ILE cc_start: 0.8657 (mp) cc_final: 0.8330 (mt) REVERT: L 10 MET cc_start: 0.5952 (ttm) cc_final: 0.5461 (ttm) REVERT: L 81 GLN cc_start: 0.7716 (mp-120) cc_final: 0.7426 (mm-40) REVERT: C 104 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.4788 (mmt) REVERT: C 166 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8119 (p) REVERT: C 221 MET cc_start: 0.7532 (tpt) cc_final: 0.7145 (tpt) REVERT: C 524 ASP cc_start: 0.7869 (m-30) cc_final: 0.7629 (p0) REVERT: G 81 GLN cc_start: 0.7837 (mp-120) cc_final: 0.7304 (mt0) REVERT: D 502 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7269 (m170) REVERT: F 7 SER cc_start: 0.8233 (t) cc_final: 0.7957 (p) REVERT: F 53 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8239 (mtmm) outliers start: 63 outliers final: 44 residues processed: 241 average time/residue: 0.2422 time to fit residues: 90.9631 Evaluate side-chains 253 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 HIS G 39 GLN D 102 HIS D 390 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 GLN D 502 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.195672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.158859 restraints weight = 180254.649| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 8.99 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16179 Z= 0.204 Angle : 0.558 7.505 22056 Z= 0.289 Chirality : 0.046 0.163 2400 Planarity : 0.004 0.057 2862 Dihedral : 4.376 18.324 2169 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.92 % Favored : 95.93 % Rotamer: Outliers : 3.71 % Allowed : 13.86 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1965 helix: 0.14 (0.58), residues: 75 sheet: -0.84 (0.18), residues: 831 loop : -0.08 (0.21), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 474 HIS 0.013 0.001 HIS D 503 PHE 0.011 0.001 PHE E 29 TYR 0.026 0.002 TYR H 51 ARG 0.004 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6861 (mp0) REVERT: A 502 HIS cc_start: 0.7592 (m-70) cc_final: 0.6125 (t-90) REVERT: A 532 ILE cc_start: 0.8645 (mp) cc_final: 0.8318 (mt) REVERT: L 39 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: L 81 GLN cc_start: 0.7639 (mp-120) cc_final: 0.7083 (mm110) REVERT: C 104 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.5561 (mmt) REVERT: C 221 MET cc_start: 0.7765 (tpt) cc_final: 0.7390 (tpt) REVERT: G 39 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: G 44 GLN cc_start: 0.7729 (mp10) cc_final: 0.7514 (mp10) REVERT: G 81 GLN cc_start: 0.7751 (mp-120) cc_final: 0.7307 (mt0) REVERT: D 502 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7633 (m170) REVERT: F 7 SER cc_start: 0.8216 (t) cc_final: 0.7951 (p) REVERT: F 53 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8230 (mtmm) REVERT: H 39 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7808 (tt0) outliers start: 64 outliers final: 50 residues processed: 237 average time/residue: 0.2429 time to fit residues: 90.4218 Evaluate side-chains 251 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 410 ASN A 475 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 81 GLN C 324 GLN C 475 ASN C 483 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN G 39 GLN D 102 HIS D 410 ASN D 475 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.185460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.147648 restraints weight = 181894.874| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 8.62 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 16179 Z= 0.451 Angle : 0.770 9.604 22056 Z= 0.406 Chirality : 0.053 0.233 2400 Planarity : 0.006 0.059 2862 Dihedral : 5.226 22.002 2169 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 5.10 % Allowed : 14.61 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1965 helix: 0.04 (0.58), residues: 75 sheet: -1.13 (0.17), residues: 891 loop : -0.33 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 474 HIS 0.026 0.002 HIS D 502 PHE 0.018 0.002 PHE L 24 TYR 0.046 0.003 TYR H 51 ARG 0.004 0.001 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 192 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 502 HIS cc_start: 0.7508 (m-70) cc_final: 0.6104 (t-90) REVERT: B 80 TYR cc_start: 0.7759 (m-80) cc_final: 0.7527 (m-80) REVERT: L 10 MET cc_start: 0.6024 (ttm) cc_final: 0.5549 (ttm) REVERT: L 81 GLN cc_start: 0.7853 (mp10) cc_final: 0.7455 (mm110) REVERT: L 96 ILE cc_start: 0.8254 (tp) cc_final: 0.8048 (tp) REVERT: C 104 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.5861 (mmt) REVERT: C 221 MET cc_start: 0.8055 (tpt) cc_final: 0.7747 (tpt) REVERT: G 81 GLN cc_start: 0.7918 (mp-120) cc_final: 0.7386 (mt0) REVERT: G 96 ILE cc_start: 0.8380 (tp) cc_final: 0.8043 (tp) REVERT: F 53 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8301 (mtmm) REVERT: F 106 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4531 (mm) outliers start: 88 outliers final: 55 residues processed: 236 average time/residue: 0.2513 time to fit residues: 94.2353 Evaluate side-chains 245 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 0.0470 chunk 86 optimal weight: 7.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 364 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C 410 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN D 410 ASN D 502 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.186952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.149183 restraints weight = 182241.646| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 8.76 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16179 Z= 0.292 Angle : 0.646 8.903 22056 Z= 0.340 Chirality : 0.049 0.179 2400 Planarity : 0.005 0.068 2862 Dihedral : 5.040 22.554 2169 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.72 % Favored : 96.13 % Rotamer: Outliers : 4.35 % Allowed : 15.88 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 1965 helix: 0.12 (0.58), residues: 78 sheet: -1.10 (0.17), residues: 888 loop : -0.35 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 474 HIS 0.011 0.001 HIS C 484 PHE 0.014 0.002 PHE E 29 TYR 0.033 0.002 TYR H 51 ARG 0.002 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 1.637 Fit side-chains REVERT: A 221 MET cc_start: 0.7814 (tpt) cc_final: 0.7474 (tpt) REVERT: A 474 TRP cc_start: 0.7585 (OUTLIER) cc_final: 0.6062 (t60) REVERT: A 502 HIS cc_start: 0.7417 (m-70) cc_final: 0.6097 (t-90) REVERT: B 80 TYR cc_start: 0.7700 (m-80) cc_final: 0.7485 (m-80) REVERT: L 81 GLN cc_start: 0.7872 (mp10) cc_final: 0.7542 (mm110) REVERT: L 96 ILE cc_start: 0.8156 (tp) cc_final: 0.7919 (tp) REVERT: C 104 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6024 (mmt) REVERT: C 166 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.7983 (m) REVERT: C 221 MET cc_start: 0.7738 (tpt) cc_final: 0.7336 (tpt) REVERT: E 53 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8304 (mttp) REVERT: G 44 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7809 (mp10) REVERT: G 81 GLN cc_start: 0.7967 (mp-120) cc_final: 0.7399 (mt0) REVERT: G 96 ILE cc_start: 0.8389 (tp) cc_final: 0.8039 (tp) REVERT: D 323 TYR cc_start: 0.8136 (t80) cc_final: 0.7857 (t80) REVERT: D 498 MET cc_start: 0.7525 (mmt) cc_final: 0.7258 (mmt) REVERT: D 581 MET cc_start: 0.7984 (ttt) cc_final: 0.7503 (ttt) REVERT: F 53 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8195 (mtmm) REVERT: F 106 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4730 (mm) outliers start: 75 outliers final: 54 residues processed: 227 average time/residue: 0.2527 time to fit residues: 88.4436 Evaluate side-chains 239 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN L 6 HIS C 410 ASN E 74 ASN D 410 ASN D 502 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.185911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.160681 restraints weight = 18145.474| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.64 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16179 Z= 0.214 Angle : 0.610 9.096 22056 Z= 0.320 Chirality : 0.047 0.217 2400 Planarity : 0.005 0.063 2862 Dihedral : 4.867 21.833 2169 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 3.94 % Allowed : 16.46 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1965 helix: 0.56 (0.58), residues: 75 sheet: -1.01 (0.17), residues: 876 loop : -0.32 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 474 HIS 0.005 0.001 HIS D 107 PHE 0.012 0.001 PHE E 29 TYR 0.027 0.002 TYR H 51 ARG 0.002 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: A 474 TRP cc_start: 0.7476 (OUTLIER) cc_final: 0.6043 (t60) REVERT: A 532 ILE cc_start: 0.8864 (mp) cc_final: 0.8561 (mt) REVERT: L 96 ILE cc_start: 0.8206 (tp) cc_final: 0.7934 (tp) REVERT: C 104 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.5536 (mmt) REVERT: C 166 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.7977 (m) REVERT: C 221 MET cc_start: 0.7706 (tpt) cc_final: 0.7370 (tpt) REVERT: C 612 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7964 (t) REVERT: E 53 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8284 (mttp) REVERT: E 74 ASN cc_start: 0.6862 (OUTLIER) cc_final: 0.6631 (t0) REVERT: G 44 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7685 (mp10) REVERT: G 81 GLN cc_start: 0.7801 (mp-120) cc_final: 0.7453 (mt0) REVERT: G 96 ILE cc_start: 0.8420 (tp) cc_final: 0.8045 (tp) REVERT: D 166 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8124 (m) REVERT: D 498 MET cc_start: 0.7266 (mmt) cc_final: 0.7057 (mmt) REVERT: D 502 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.6416 (t-90) REVERT: D 581 MET cc_start: 0.7918 (ttt) cc_final: 0.7481 (ttt) REVERT: F 53 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8237 (mtmm) REVERT: F 106 LEU cc_start: 0.4569 (OUTLIER) cc_final: 0.4315 (mm) outliers start: 68 outliers final: 53 residues processed: 217 average time/residue: 0.2449 time to fit residues: 84.2473 Evaluate side-chains 237 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 147 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN E 74 ASN D 410 ASN D 502 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.188809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.152690 restraints weight = 178863.955| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 8.49 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16179 Z= 0.198 Angle : 0.592 8.507 22056 Z= 0.310 Chirality : 0.046 0.175 2400 Planarity : 0.005 0.056 2862 Dihedral : 4.766 21.229 2169 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 4.00 % Allowed : 16.99 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.20), residues: 1965 helix: 0.73 (0.58), residues: 75 sheet: -0.92 (0.18), residues: 873 loop : -0.28 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 474 HIS 0.011 0.001 HIS D 502 PHE 0.012 0.001 PHE E 29 TYR 0.024 0.002 TYR H 51 ARG 0.002 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 1.878 Fit side-chains revert: symmetry clash REVERT: A 532 ILE cc_start: 0.8763 (mp) cc_final: 0.8515 (mt) REVERT: L 94 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7032 (tt) REVERT: L 96 ILE cc_start: 0.8155 (tp) cc_final: 0.7912 (tp) REVERT: C 104 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.5743 (mmt) REVERT: C 166 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8050 (m) REVERT: C 221 MET cc_start: 0.7582 (tpt) cc_final: 0.7246 (tpt) REVERT: C 612 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7732 (t) REVERT: E 53 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8084 (mttp) REVERT: G 44 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7811 (mp10) REVERT: G 81 GLN cc_start: 0.7820 (mp-120) cc_final: 0.7311 (mt0) REVERT: G 96 ILE cc_start: 0.8352 (tp) cc_final: 0.8006 (tp) REVERT: D 166 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8212 (m) REVERT: D 502 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.6204 (t-90) REVERT: D 581 MET cc_start: 0.7991 (ttt) cc_final: 0.7487 (ttt) REVERT: F 53 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8134 (mtmm) REVERT: F 106 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4996 (mm) outliers start: 69 outliers final: 53 residues processed: 224 average time/residue: 0.2319 time to fit residues: 82.5607 Evaluate side-chains 244 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 33 optimal weight: 3.9990 chunk 114 optimal weight: 0.0270 chunk 3 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 475 ASN E 74 ASN D 410 ASN D 502 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.188462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.186522 restraints weight = 18061.132| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 0.10 r_work: 0.3939 rms_B_bonded: 0.38 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 0.92 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16179 Z= 0.173 Angle : 0.576 8.273 22056 Z= 0.300 Chirality : 0.045 0.170 2400 Planarity : 0.005 0.055 2862 Dihedral : 4.627 20.541 2169 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 3.36 % Allowed : 17.57 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1965 helix: 0.96 (0.58), residues: 75 sheet: -0.84 (0.18), residues: 879 loop : -0.20 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 474 HIS 0.019 0.001 HIS D 502 PHE 0.011 0.001 PHE A 92 TYR 0.019 0.001 TYR D 178 ARG 0.002 0.000 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 1.679 Fit side-chains REVERT: A 532 ILE cc_start: 0.8866 (mp) cc_final: 0.8590 (mt) REVERT: L 94 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7092 (tt) REVERT: L 96 ILE cc_start: 0.8222 (tp) cc_final: 0.7962 (tp) REVERT: C 104 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.5287 (mmt) REVERT: C 166 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8010 (m) REVERT: C 221 MET cc_start: 0.7633 (tpt) cc_final: 0.7346 (tpt) REVERT: C 612 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7656 (t) REVERT: E 53 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8367 (mttp) REVERT: G 44 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7631 (mp10) REVERT: G 81 GLN cc_start: 0.7735 (mp-120) cc_final: 0.7360 (mt0) REVERT: G 96 ILE cc_start: 0.8385 (tp) cc_final: 0.8022 (tp) REVERT: D 166 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8111 (m) REVERT: D 502 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.6385 (t-90) REVERT: D 581 MET cc_start: 0.7854 (ttt) cc_final: 0.7427 (ttt) outliers start: 58 outliers final: 49 residues processed: 217 average time/residue: 0.2240 time to fit residues: 77.7981 Evaluate side-chains 235 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 403 ASN Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 580 MET Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 128 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 475 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.188264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.186578 restraints weight = 18046.399| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.09 r_work: 0.3941 rms_B_bonded: 0.35 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.267 16179 Z= 0.329 Angle : 0.877 59.186 22056 Z= 0.536 Chirality : 0.057 1.501 2400 Planarity : 0.007 0.153 2862 Dihedral : 4.662 20.700 2169 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 3.30 % Allowed : 17.91 % Favored : 78.78 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1965 helix: 0.97 (0.58), residues: 75 sheet: -0.83 (0.18), residues: 879 loop : -0.20 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 474 HIS 0.203 0.003 HIS D 502 PHE 0.010 0.001 PHE E 29 TYR 0.066 0.002 TYR A 97 ARG 0.002 0.000 ARG D 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5081.12 seconds wall clock time: 94 minutes 11.29 seconds (5651.29 seconds total)