Starting phenix.real_space_refine on Sun Aug 24 00:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3r_38896/08_2025/8y3r_38896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3r_38896/08_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_38896/08_2025/8y3r_38896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3r_38896/08_2025/8y3r_38896.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3r_38896/08_2025/8y3r_38896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3r_38896/08_2025/8y3r_38896.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.16, per 1000 atoms: 0.20 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: 0.97 Conformation dependent library (CDL) restraints added in 530.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.49 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: 2.47 Time building geometry restraints manager: 1.33 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- 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 16188 Z= 0.202 Angle : 0.617 11.615 22074 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG C 212 TYR 0.037 0.001 TYR D 203 PHE 0.013 0.001 PHE C 557 TRP 0.009 0.001 TRP D 330 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00329 (16179) covalent geometry : angle 0.61651 (22056) SS BOND : bond 0.00168 ( 9) SS BOND : angle 0.63151 ( 18) hydrogen bonds : bond 0.15511 ( 368) hydrogen bonds : angle 6.65505 ( 918) *********************** 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 : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6269 (mtmm) cc_final: 0.5906 (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: 0.7967 (t) REVERT: L 81 GLN cc_start: 0.7508 (mp-120) cc_final: 0.6871 (mt0) REVERT: C 209 THR cc_start: 0.7213 (m) cc_final: 0.6537 (p) REVERT: C 581 MET cc_start: 0.6300 (ttt) cc_final: 0.5897 (ttt) REVERT: G 81 GLN cc_start: 0.7643 (mp-120) cc_final: 0.7270 (mt0) REVERT: G 91 THR cc_start: 0.8116 (t) cc_final: 0.7849 (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: 0.7662 (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: 0.1069 time to fit residues: 51.4319 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 : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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 C 484 HIS C 502 HIS G 33 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS D 484 HIS D 502 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.202882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.167429 restraints weight = 180631.772| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 9.43 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16188 Z= 0.127 Angle : 0.590 6.926 22074 Z= 0.307 Chirality : 0.047 0.228 2400 Planarity : 0.005 0.074 2862 Dihedral : 4.425 19.004 2169 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.09 % Allowed : 9.28 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1965 helix: -0.63 (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 ARG 0.006 0.000 ARG L 47 TYR 0.021 0.001 TYR H 51 PHE 0.011 0.001 PHE E 29 TRP 0.009 0.001 TRP C 396 HIS 0.005 0.001 HIS D 482 Details of bonding type rmsd covalent geometry : bond 0.00297 (16179) covalent geometry : angle 0.58957 (22056) SS BOND : bond 0.00293 ( 9) SS BOND : angle 0.65222 ( 18) hydrogen bonds : bond 0.03436 ( 368) hydrogen bonds : angle 5.19736 ( 918) *********************** 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 273 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.8359 (m) cc_final: 0.7710 (p) REVERT: A 502 HIS cc_start: 0.7223 (m-70) cc_final: 0.5803 (t-90) REVERT: B 7 SER cc_start: 0.8117 (t) cc_final: 0.7903 (p) REVERT: L 44 GLN cc_start: 0.7559 (mm110) cc_final: 0.7168 (mp10) REVERT: L 81 GLN cc_start: 0.7684 (mp-120) cc_final: 0.7282 (mt0) REVERT: C 209 THR cc_start: 0.8128 (m) cc_final: 0.7565 (p) REVERT: C 221 MET cc_start: 0.7542 (tpt) cc_final: 0.7175 (tpt) REVERT: G 44 GLN cc_start: 0.7354 (mp10) cc_final: 0.7134 (mp10) REVERT: G 81 GLN cc_start: 0.7888 (mp-120) cc_final: 0.7494 (mt0) REVERT: D 502 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7167 (m170) REVERT: F 7 SER cc_start: 0.8242 (t) cc_final: 0.7891 (p) REVERT: F 53 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8247 (mtmm) outliers start: 36 outliers final: 24 residues processed: 249 average time/residue: 0.0986 time to fit residues: 38.3314 Evaluate side-chains 230 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 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 149 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 390 ASN ** 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 = 0.4090 r_free = 0.4090 target = 0.199521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.163664 restraints weight = 180047.343| |-----------------------------------------------------------------------------| 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: 0.7599 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16188 Z= 0.120 Angle : 0.560 7.210 22074 Z= 0.291 Chirality : 0.046 0.179 2400 Planarity : 0.004 0.066 2862 Dihedral : 4.376 18.101 2169 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.07 % Allowed : 11.94 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1965 helix: -0.25 (0.57), residues: 75 sheet: -0.86 (0.18), residues: 834 loop : -0.17 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.022 0.002 TYR H 51 PHE 0.012 0.001 PHE E 29 TRP 0.009 0.001 TRP A 330 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00286 (16179) covalent geometry : angle 0.56008 (22056) SS BOND : bond 0.00325 ( 9) SS BOND : angle 0.45168 ( 18) hydrogen bonds : bond 0.03022 ( 368) hydrogen bonds : angle 4.93652 ( 918) *********************** 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 268 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6928 (mp0) REVERT: A 502 HIS cc_start: 0.7323 (m-70) cc_final: 0.6053 (t-90) REVERT: A 532 ILE cc_start: 0.8533 (mp) cc_final: 0.8163 (mt) REVERT: L 44 GLN cc_start: 0.7746 (mm110) cc_final: 0.7371 (mp10) REVERT: L 81 GLN cc_start: 0.7688 (mp-120) cc_final: 0.7360 (mm-40) REVERT: L 105 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7236 (p) REVERT: C 209 THR cc_start: 0.8480 (m) cc_final: 0.7929 (p) REVERT: C 221 MET cc_start: 0.7467 (tpt) cc_final: 0.6966 (tpt) REVERT: G 44 GLN cc_start: 0.7599 (mp10) cc_final: 0.7326 (mp10) REVERT: G 81 GLN cc_start: 0.7681 (mp-120) cc_final: 0.7254 (mt0) REVERT: D 88 ASN cc_start: 0.8799 (m110) cc_final: 0.8583 (m-40) REVERT: D 502 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7243 (m170) REVERT: F 7 SER cc_start: 0.8277 (t) cc_final: 0.7979 (p) REVERT: F 53 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8256 (mtmm) outliers start: 53 outliers final: 40 residues processed: 238 average time/residue: 0.0996 time to fit residues: 37.4916 Evaluate side-chains 245 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 521 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 L residue 105 THR Chi-restraints excluded: chain L residue 108 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 E residue 84 ASN 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 166 VAL 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 154 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 488 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN C 102 HIS C 390 ASN G 39 GLN G 106 HIS D 102 HIS D 390 ASN D 410 ASN D 475 ASN D 503 HIS F 74 ASN H 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.192168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.156103 restraints weight = 182120.194| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 9.01 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16188 Z= 0.170 Angle : 0.619 8.096 22074 Z= 0.322 Chirality : 0.048 0.179 2400 Planarity : 0.005 0.067 2862 Dihedral : 4.679 19.393 2169 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.97 % Favored : 95.88 % Rotamer: Outliers : 4.41 % Allowed : 13.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1965 helix: -0.36 (0.55), residues: 75 sheet: -0.90 (0.18), residues: 873 loop : -0.15 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 511 TYR 0.033 0.002 TYR H 51 PHE 0.015 0.002 PHE E 29 TRP 0.014 0.002 TRP D 474 HIS 0.029 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00413 (16179) covalent geometry : angle 0.61879 (22056) SS BOND : bond 0.00441 ( 9) SS BOND : angle 0.47866 ( 18) hydrogen bonds : bond 0.03278 ( 368) hydrogen bonds : angle 4.99677 ( 918) *********************** 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 289 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 213 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6789 (mp0) REVERT: A 502 HIS cc_start: 0.7432 (m-70) cc_final: 0.6128 (t-90) REVERT: A 532 ILE cc_start: 0.8792 (mp) cc_final: 0.8438 (mt) REVERT: L 10 MET cc_start: 0.6083 (ttm) cc_final: 0.5569 (ttm) REVERT: L 39 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: L 44 GLN cc_start: 0.8086 (mm110) cc_final: 0.7842 (mp10) REVERT: L 81 GLN cc_start: 0.7776 (mp-120) cc_final: 0.7231 (mm110) REVERT: C 104 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.5604 (mmt) REVERT: C 181 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6743 (mp0) REVERT: C 221 MET cc_start: 0.7617 (tpt) cc_final: 0.7162 (tpt) REVERT: G 39 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: G 81 GLN cc_start: 0.7861 (mp-120) cc_final: 0.7354 (mt0) REVERT: G 96 ILE cc_start: 0.8317 (tp) cc_final: 0.7975 (tp) REVERT: D 88 ASN cc_start: 0.8947 (m110) cc_final: 0.8613 (m-40) REVERT: F 7 SER cc_start: 0.8155 (t) cc_final: 0.7915 (p) REVERT: F 53 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8288 (mtmm) REVERT: H 39 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7835 (tt0) outliers start: 76 outliers final: 48 residues processed: 250 average time/residue: 0.0891 time to fit residues: 35.1259 Evaluate side-chains 247 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 21 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 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 E residue 46 GLU 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 84 ASN 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 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 403 ASN Chi-restraints excluded: chain D residue 473 THR 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 6 HIS 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 Chi-restraints excluded: chain H residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN C 102 HIS C 324 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN D 102 HIS D 410 ASN D 499 GLN D 502 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 39 GLN H 106 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.192219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.155254 restraints weight = 181031.687| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 8.95 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16188 Z= 0.136 Angle : 0.579 8.021 22074 Z= 0.302 Chirality : 0.046 0.170 2400 Planarity : 0.004 0.062 2862 Dihedral : 4.592 19.945 2169 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 4.06 % Allowed : 14.78 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.20), residues: 1965 helix: 0.52 (0.57), residues: 75 sheet: -0.91 (0.18), residues: 873 loop : -0.05 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 511 TYR 0.026 0.002 TYR H 51 PHE 0.013 0.001 PHE E 29 TRP 0.013 0.001 TRP D 474 HIS 0.005 0.001 HIS D 565 Details of bonding type rmsd covalent geometry : bond 0.00329 (16179) covalent geometry : angle 0.57939 (22056) SS BOND : bond 0.00358 ( 9) SS BOND : angle 0.37161 ( 18) hydrogen bonds : bond 0.03031 ( 368) hydrogen bonds : angle 4.95029 ( 918) *********************** 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 278 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6914 (mp0) REVERT: A 502 HIS cc_start: 0.7542 (m-70) cc_final: 0.6104 (t-90) REVERT: A 532 ILE cc_start: 0.8703 (mp) cc_final: 0.8418 (mt) REVERT: L 39 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: L 44 GLN cc_start: 0.8182 (mm110) cc_final: 0.7925 (mp10) REVERT: L 81 GLN cc_start: 0.7677 (mp-120) cc_final: 0.7187 (mm110) REVERT: L 96 ILE cc_start: 0.7980 (tp) cc_final: 0.7744 (tp) REVERT: C 104 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.5916 (mmt) REVERT: C 166 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.7931 (m) REVERT: C 221 MET cc_start: 0.7771 (tpt) cc_final: 0.7433 (tpt) REVERT: G 39 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: G 81 GLN cc_start: 0.7712 (mp-120) cc_final: 0.7264 (mt0) REVERT: G 96 ILE cc_start: 0.8261 (tp) cc_final: 0.7922 (tp) REVERT: D 221 MET cc_start: 0.7545 (tpt) cc_final: 0.7205 (tpt) REVERT: D 581 MET cc_start: 0.7958 (ttt) cc_final: 0.7380 (ttt) REVERT: F 7 SER cc_start: 0.8239 (t) cc_final: 0.8029 (p) REVERT: F 53 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8271 (mtmm) REVERT: F 106 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4550 (mm) REVERT: H 39 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: H 44 GLN cc_start: 0.7955 (mp-120) cc_final: 0.7743 (mp10) outliers start: 70 outliers final: 52 residues processed: 238 average time/residue: 0.0929 time to fit residues: 34.7084 Evaluate side-chains 257 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 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 B residue 103 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 39 GLN 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 46 GLU 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 106 LEU 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 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 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 F residue 106 LEU Chi-restraints excluded: chain H residue 6 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 41 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 475 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 81 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN C 488 HIS E 74 ASN G 39 GLN D 410 ASN D 488 HIS D 502 HIS F 74 ASN H 32 ASN H 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.184705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.146897 restraints weight = 182134.555| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 8.67 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16188 Z= 0.269 Angle : 0.743 9.128 22074 Z= 0.390 Chirality : 0.052 0.210 2400 Planarity : 0.006 0.064 2862 Dihedral : 5.223 22.045 2169 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.19 % Favored : 94.66 % Rotamer: Outliers : 4.58 % Allowed : 15.48 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.19), residues: 1965 helix: -0.00 (0.58), residues: 75 sheet: -1.16 (0.17), residues: 891 loop : -0.37 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 212 TYR 0.042 0.003 TYR H 51 PHE 0.019 0.002 PHE E 29 TRP 0.024 0.002 TRP D 474 HIS 0.035 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00663 (16179) covalent geometry : angle 0.74324 (22056) SS BOND : bond 0.00641 ( 9) SS BOND : angle 0.71477 ( 18) hydrogen bonds : bond 0.04074 ( 368) hydrogen bonds : angle 5.38682 ( 918) *********************** 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 276 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7173 (mt-10) REVERT: A 221 MET cc_start: 0.8002 (tpt) cc_final: 0.7607 (tpt) REVERT: A 502 HIS cc_start: 0.7517 (m-70) cc_final: 0.6095 (t-90) REVERT: L 44 GLN cc_start: 0.8302 (mm110) cc_final: 0.8055 (mp10) REVERT: L 47 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7943 (ptm160) REVERT: L 81 GLN cc_start: 0.7865 (mp10) cc_final: 0.7502 (mm110) REVERT: L 96 ILE cc_start: 0.8230 (tp) cc_final: 0.7997 (tp) REVERT: C 104 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.5886 (mmt) REVERT: C 221 MET cc_start: 0.8013 (tpt) cc_final: 0.7705 (tpt) REVERT: G 81 GLN cc_start: 0.7942 (mp-120) cc_final: 0.7362 (mt0) REVERT: G 96 ILE cc_start: 0.8412 (tp) cc_final: 0.8058 (tp) REVERT: D 323 TYR cc_start: 0.8098 (t80) cc_final: 0.7816 (t80) REVERT: D 581 MET cc_start: 0.8162 (ttt) cc_final: 0.7639 (ttt) REVERT: F 53 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8280 (mtmm) REVERT: F 106 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.4559 (mm) REVERT: H 107 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6355 (tp) outliers start: 79 outliers final: 56 residues processed: 232 average time/residue: 0.0935 time to fit residues: 34.0512 Evaluate side-chains 243 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 536 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 623 LEU 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 39 GLN 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 C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 327 LEU 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 529 THR Chi-restraints excluded: chain E residue 7 SER 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 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 41 THR 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 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 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 74 ASN Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain H residue 6 HIS Chi-restraints excluded: chain H residue 22 CYS 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 Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** B 35 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 C 475 ASN E 74 ASN D 410 ASN F 74 ASN H 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.187076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.185860 restraints weight = 18027.672| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 0.06 r_work: 0.3951 rms_B_bonded: 0.24 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 0.72 restraints_weight: 0.2500 r_work: 0.3717 rms_B_bonded: 4.22 restraints_weight: 0.1250 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16188 Z= 0.125 Angle : 0.588 8.798 22074 Z= 0.309 Chirality : 0.046 0.179 2400 Planarity : 0.005 0.059 2862 Dihedral : 4.824 21.495 2169 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 4.12 % Allowed : 16.35 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.19), residues: 1965 helix: 0.48 (0.57), residues: 75 sheet: -1.00 (0.17), residues: 897 loop : -0.28 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 43 TYR 0.023 0.002 TYR H 51 PHE 0.013 0.001 PHE E 29 TRP 0.019 0.001 TRP D 474 HIS 0.004 0.001 HIS L 6 Details of bonding type rmsd covalent geometry : bond 0.00298 (16179) covalent geometry : angle 0.58814 (22056) SS BOND : bond 0.00338 ( 9) SS BOND : angle 0.41424 ( 18) hydrogen bonds : bond 0.02998 ( 368) hydrogen bonds : angle 5.12439 ( 918) *********************** 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: 71 poor density : 197 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 474 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.6503 (t60) REVERT: A 502 HIS cc_start: 0.7739 (m-70) cc_final: 0.6305 (t-90) REVERT: A 532 ILE cc_start: 0.8965 (mp) cc_final: 0.8726 (mt) REVERT: A 536 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6323 (tt) REVERT: L 96 ILE cc_start: 0.8272 (tp) cc_final: 0.7985 (tp) REVERT: C 92 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.5686 (t80) REVERT: C 104 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.5829 (mmt) REVERT: C 166 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8110 (m) REVERT: C 221 MET cc_start: 0.7919 (tpt) cc_final: 0.7614 (tpt) REVERT: E 53 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8484 (mttp) REVERT: G 39 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7954 (tt0) REVERT: G 81 GLN cc_start: 0.7941 (mp-120) cc_final: 0.7484 (mt0) REVERT: G 96 ILE cc_start: 0.8427 (tp) cc_final: 0.8018 (tp) REVERT: D 166 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8223 (m) REVERT: D 498 MET cc_start: 0.7898 (mmt) cc_final: 0.7542 (mmt) REVERT: D 532 ILE cc_start: 0.8782 (mp) cc_final: 0.8524 (mt) REVERT: D 581 MET cc_start: 0.8081 (ttt) cc_final: 0.7681 (ttt) REVERT: F 53 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8329 (mtmm) REVERT: F 74 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6587 (t0) REVERT: F 106 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4778 (mm) outliers start: 71 outliers final: 42 residues processed: 236 average time/residue: 0.0962 time to fit residues: 36.3275 Evaluate side-chains 235 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 54 ILE 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 97 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain L residue 22 CYS 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 C residue 92 PHE 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 529 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 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 58 THR 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 473 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain H residue 6 HIS 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 Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 53 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 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 364 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C 410 ASN E 74 ASN D 410 ASN D 502 HIS F 74 ASN H 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.189265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.151560 restraints weight = 181820.353| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 8.97 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16188 Z= 0.124 Angle : 0.598 8.754 22074 Z= 0.312 Chirality : 0.047 0.209 2400 Planarity : 0.005 0.057 2862 Dihedral : 4.755 20.814 2169 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.22 % Favored : 95.67 % Rotamer: Outliers : 4.00 % Allowed : 16.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1965 helix: 0.67 (0.57), residues: 75 sheet: -0.92 (0.18), residues: 873 loop : -0.27 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 72 TYR 0.024 0.002 TYR H 51 PHE 0.012 0.001 PHE E 29 TRP 0.015 0.001 TRP C 474 HIS 0.004 0.001 HIS L 6 Details of bonding type rmsd covalent geometry : bond 0.00297 (16179) covalent geometry : angle 0.59839 (22056) SS BOND : bond 0.00325 ( 9) SS BOND : angle 0.35381 ( 18) hydrogen bonds : bond 0.02914 ( 368) hydrogen bonds : angle 5.01816 ( 918) *********************** 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 268 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 199 time to evaluate : 0.423 Fit side-chains REVERT: A 474 TRP cc_start: 0.7368 (OUTLIER) cc_final: 0.5862 (t60) REVERT: A 502 HIS cc_start: 0.7500 (m-70) cc_final: 0.6088 (t-90) REVERT: A 532 ILE cc_start: 0.8687 (mp) cc_final: 0.8483 (mt) REVERT: A 536 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.5931 (tt) REVERT: L 44 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: L 96 ILE cc_start: 0.8104 (tp) cc_final: 0.7848 (tp) REVERT: C 92 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.5283 (t80) REVERT: C 104 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.5774 (mmt) REVERT: C 166 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8025 (m) REVERT: C 221 MET cc_start: 0.7641 (tpt) cc_final: 0.7291 (tpt) REVERT: E 53 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8336 (mttp) REVERT: G 39 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7992 (tt0) REVERT: G 44 GLN cc_start: 0.7902 (mp10) cc_final: 0.7671 (mm-40) REVERT: G 81 GLN cc_start: 0.8006 (mp-120) cc_final: 0.7327 (mt0) REVERT: G 96 ILE cc_start: 0.8386 (tp) cc_final: 0.8028 (tp) REVERT: D 166 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8158 (m) REVERT: D 532 ILE cc_start: 0.8516 (mp) cc_final: 0.8270 (mt) REVERT: D 581 MET cc_start: 0.7976 (ttt) cc_final: 0.7457 (ttt) REVERT: F 53 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8163 (mtmm) REVERT: F 74 ASN cc_start: 0.6195 (OUTLIER) cc_final: 0.5991 (t0) REVERT: F 106 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4873 (mm) outliers start: 69 outliers final: 53 residues processed: 232 average time/residue: 0.0922 time to fit residues: 34.2698 Evaluate side-chains 250 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 B residue 97 VAL 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 44 GLN Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain C residue 92 PHE 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 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 41 THR Chi-restraints excluded: chain G residue 58 THR 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 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 F residue 7 SER Chi-restraints excluded: chain F residue 46 GLU 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 74 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain H residue 6 HIS 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 Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 67 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 416 ASN A 475 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 475 ASN E 74 ASN D 410 ASN F 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.185399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.184582 restraints weight = 18410.411| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 0.04 r_work: 0.3936 rms_B_bonded: 0.18 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 0.64 restraints_weight: 0.2500 r_work: 0.3759 rms_B_bonded: 3.42 restraints_weight: 0.1250 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16188 Z= 0.179 Angle : 0.652 8.874 22074 Z= 0.341 Chirality : 0.049 0.179 2400 Planarity : 0.005 0.057 2862 Dihedral : 4.920 21.213 2169 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.63 % Favored : 95.27 % Rotamer: Outliers : 4.17 % Allowed : 16.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1965 helix: 0.50 (0.58), residues: 75 sheet: -0.99 (0.17), residues: 888 loop : -0.34 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 72 TYR 0.032 0.002 TYR H 51 PHE 0.016 0.001 PHE E 29 TRP 0.017 0.001 TRP C 474 HIS 0.022 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00436 (16179) covalent geometry : angle 0.65233 (22056) SS BOND : bond 0.00413 ( 9) SS BOND : angle 0.34308 ( 18) hydrogen bonds : bond 0.03313 ( 368) hydrogen bonds : angle 5.08277 ( 918) *********************** 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 255 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 183 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 474 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.6578 (t60) REVERT: A 532 ILE cc_start: 0.8977 (mp) cc_final: 0.8724 (mt) REVERT: L 44 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: L 94 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7543 (tt) REVERT: L 96 ILE cc_start: 0.8362 (tp) cc_final: 0.8067 (tp) REVERT: C 104 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.5635 (mmt) REVERT: C 221 MET cc_start: 0.7866 (tpt) cc_final: 0.7567 (tpt) REVERT: E 53 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8478 (mttp) REVERT: E 74 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6804 (t0) REVERT: G 39 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8066 (tt0) REVERT: G 81 GLN cc_start: 0.7892 (mp-120) cc_final: 0.7442 (mt0) REVERT: G 96 ILE cc_start: 0.8499 (tp) cc_final: 0.8076 (tp) REVERT: D 166 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8253 (m) REVERT: D 498 MET cc_start: 0.7758 (mmt) cc_final: 0.7490 (mmt) REVERT: D 502 HIS cc_start: 0.7938 (m-70) cc_final: 0.6524 (t-90) REVERT: D 581 MET cc_start: 0.8020 (ttt) cc_final: 0.7615 (ttt) REVERT: F 53 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8278 (mtmm) REVERT: F 106 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4691 (mm) outliers start: 72 outliers final: 54 residues processed: 219 average time/residue: 0.0972 time to fit residues: 33.5522 Evaluate side-chains 243 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 97 VAL 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 44 GLN 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 C residue 104 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 327 LEU 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 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 58 THR 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 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 529 THR Chi-restraints excluded: chain D residue 580 MET 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 103 THR 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 112 optimal weight: 0.9990 chunk 105 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 160 optimal weight: 0.0370 chunk 15 optimal weight: 0.0000 chunk 142 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.2822 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 475 ASN E 74 ASN D 410 ASN D 475 ASN F 74 ASN H 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.190684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.188511 restraints weight = 18162.660| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 0.10 r_work: 0.3948 rms_B_bonded: 0.30 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 0.78 restraints_weight: 0.2500 r_work: 0.3797 rms_B_bonded: 2.70 restraints_weight: 0.1250 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16188 Z= 0.101 Angle : 0.563 8.259 22074 Z= 0.295 Chirality : 0.045 0.218 2400 Planarity : 0.005 0.053 2862 Dihedral : 4.553 20.145 2169 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.22 % Favored : 95.67 % Rotamer: Outliers : 2.90 % Allowed : 18.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1965 helix: 1.01 (0.58), residues: 75 sheet: -0.87 (0.18), residues: 864 loop : -0.17 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.019 0.001 TYR D 178 PHE 0.012 0.001 PHE A 92 TRP 0.013 0.001 TRP C 474 HIS 0.006 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00234 (16179) covalent geometry : angle 0.56281 (22056) SS BOND : bond 0.00261 ( 9) SS BOND : angle 0.49611 ( 18) hydrogen bonds : bond 0.02625 ( 368) hydrogen bonds : angle 4.85182 ( 918) ********************** 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 242 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 166 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8024 (m) REVERT: A 474 TRP cc_start: 0.7525 (OUTLIER) cc_final: 0.6263 (t60) REVERT: A 536 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6191 (tt) REVERT: L 44 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: L 96 ILE cc_start: 0.8227 (tp) cc_final: 0.7939 (tp) REVERT: C 104 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.5585 (mmt) REVERT: C 166 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8022 (m) REVERT: C 221 MET cc_start: 0.7769 (tpt) cc_final: 0.7469 (tpt) REVERT: G 39 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7945 (tt0) REVERT: G 81 GLN cc_start: 0.7926 (mp-120) cc_final: 0.7440 (mt0) REVERT: G 96 ILE cc_start: 0.8383 (tp) cc_final: 0.7990 (tp) REVERT: D 166 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8180 (m) REVERT: D 502 HIS cc_start: 0.7582 (m-70) cc_final: 0.6184 (t-90) REVERT: D 532 ILE cc_start: 0.8653 (mp) cc_final: 0.8406 (mt) REVERT: D 581 MET cc_start: 0.7954 (ttt) cc_final: 0.7512 (ttt) REVERT: F 53 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8271 (mtmm) REVERT: H 44 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7811 (mp10) outliers start: 50 outliers final: 35 residues processed: 220 average time/residue: 0.0944 time to fit residues: 33.3604 Evaluate side-chains 221 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 536 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 90 CYS 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 529 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 58 THR 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 410 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 580 MET 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 71 SER Chi-restraints excluded: chain F residue 74 ASN 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 41 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 112 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.0270 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN E 74 ASN D 475 ASN H 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.189456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.187152 restraints weight = 18167.153| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 0.13 r_work: 0.3929 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 16188 Z= 0.218 Angle : 0.979 59.137 22074 Z= 0.603 Chirality : 0.075 2.875 2400 Planarity : 0.007 0.245 2862 Dihedral : 4.604 24.998 2169 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.55 % Allowed : 18.84 % Favored : 78.61 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1965 helix: 1.04 (0.58), residues: 75 sheet: -0.87 (0.18), residues: 864 loop : -0.17 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.019 0.001 TYR D 178 PHE 0.010 0.001 PHE E 29 TRP 0.011 0.001 TRP C 474 HIS 0.375 0.004 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00376 (16179) covalent geometry : angle 0.97929 (22056) SS BOND : bond 0.00380 ( 9) SS BOND : angle 0.46696 ( 18) hydrogen bonds : bond 0.02643 ( 368) hydrogen bonds : angle 4.85254 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.72 seconds wall clock time: 41 minutes 22.76 seconds (2482.76 seconds total)