Starting phenix.real_space_refine on Tue Nov 18 19:57:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3p_38894/11_2025/8y3p_38894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3p_38894/11_2025/8y3p_38894.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/8y3p_38894/11_2025/8y3p_38894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3p_38894/11_2025/8y3p_38894.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3p_38894/11_2025/8y3p_38894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3p_38894/11_2025/8y3p_38894.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= 0.004 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 72 5.16 5 C 10860 2.51 5 N 2946 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17028 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "G" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "H" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.14, per 1000 atoms: 0.24 Number of scatterers: 17028 At special positions: 0 Unit cell: (107, 109, 142, 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 72 16.00 O 3150 8.00 N 2946 7.00 C 10860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 89 " 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: 1.22 Conformation dependent library (CDL) restraints added in 861.9 milliseconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 9.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.839A pdb=" N THR G 91 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.656A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 80 through 84' Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.511A pdb=" N ALA A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) 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 555 through 560 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 567 through 571 removed outlier: 4.037A pdb=" N ALA A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 571 " --> pdb=" O GLY A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.590A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.853A pdb=" N THR D 91 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.619A pdb=" N ASP F 83 " --> pdb=" O GLN F 80 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU F 84 " --> pdb=" O ALA F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 84' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 220 through 228 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 555 through 560 Processing helix chain 'C' and resid 560 through 566 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.880A pdb=" N THR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.501A pdb=" N TYR H 33 " --> pdb=" O THR H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.617A pdb=" N ASP H 83 " --> pdb=" O GLN H 80 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU H 84 " --> pdb=" O ALA H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 80 through 84' Processing sheet with id=AA1, first strand: chain 'B' and resid 74 through 77 removed outlier: 5.430A pdb=" N ASN B 409 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 109 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP B 103 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU B 417 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE B 101 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET B 104 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.687A pdb=" N ASN B 190 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 201 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 128 Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 158 removed outlier: 7.207A pdb=" N ARG B 389 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 522 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 241 removed outlier: 6.474A pdb=" N ASN B 309 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 307 " --> pdb=" O PRO B 240 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 307 through 314 current: chain 'A' and resid 308 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 308 through 314 current: chain 'C' and resid 307 through 314 Processing sheet with id=AA8, first strand: chain 'B' and resid 443 through 446 Processing sheet with id=AA9, first strand: chain 'B' and resid 454 through 455 removed outlier: 5.418A pdb=" N ILE B 540 " --> pdb=" O LYS B 552 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 498 Processing sheet with id=AB2, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain 'G' and resid 34 through 39 removed outlier: 7.265A pdb=" N ILE G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 50 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR G 59 " --> pdb=" O VAL G 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 60 current: chain 'G' and resid 110 through 114 Processing sheet with id=AB4, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 8 through 11 current: chain 'L' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 49 current: chain 'L' and resid 97 through 100 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 74 through 77 removed outlier: 5.311A pdb=" N ASN A 409 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE A 109 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP A 103 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU A 417 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE A 101 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N MET A 104 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.669A pdb=" N ASN A 190 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 201 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.637A pdb=" N TYR A 173 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AC1, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.259A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 522 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AC3, first strand: chain 'A' and resid 443 through 446 Processing sheet with id=AC4, first strand: chain 'A' and resid 454 through 455 removed outlier: 5.318A pdb=" N ILE A 540 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 528 through 534 removed outlier: 4.028A pdb=" N ASN A 495 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS C 246 " --> pdb=" O ASN A 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 12 current: chain 'D' and resid 45 through 51 removed outlier: 3.656A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 60 current: chain 'D' and resid 110 through 114 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'F' and resid 8 through 11 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 8 through 11 current: chain 'F' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 46 through 49 current: chain 'F' and resid 97 through 100 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 74 through 77 removed outlier: 5.329A pdb=" N ASN C 409 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE C 109 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP C 103 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU C 417 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N PHE C 101 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N MET C 104 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 89 through 93 removed outlier: 3.660A pdb=" N ASN C 190 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP C 201 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.573A pdb=" N TYR C 173 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 126 through 128 Processing sheet with id=AD5, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.210A pdb=" N ARG C 389 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 522 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 176 through 177 Processing sheet with id=AD7, first strand: chain 'C' and resid 443 through 446 Processing sheet with id=AD8, first strand: chain 'C' and resid 454 through 455 removed outlier: 5.303A pdb=" N ILE C 540 " --> pdb=" O LYS C 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 492 through 498 Processing sheet with id=AE1, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 12 current: chain 'E' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 51 current: chain 'E' and resid 110 through 114 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AE4, first strand: chain 'H' and resid 8 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 8 through 11 current: chain 'H' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 46 through 49 current: chain 'H' and resid 97 through 100 No H-bonds generated for sheet with id=AE4 396 hydrogen bonds defined for protein. 999 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: 2.97 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5512 1.34 - 1.46: 4221 1.46 - 1.58: 7670 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 17508 Sorted by residual: bond pdb=" C LEU G 106 " pdb=" N PRO G 107 " ideal model delta sigma weight residual 1.337 1.370 -0.033 9.80e-03 1.04e+04 1.14e+01 bond pdb=" C LEU D 106 " pdb=" N PRO D 107 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.19e-02 7.06e+03 9.36e+00 bond pdb=" C LEU E 106 " pdb=" N PRO E 107 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" C ASP B 159 " pdb=" N PRO B 160 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.95e+00 bond pdb=" C ASP A 159 " pdb=" N PRO A 160 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.19e-02 7.06e+03 3.55e+00 ... (remaining 17503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 23212 2.06 - 4.12: 514 4.12 - 6.19: 95 6.19 - 8.25: 22 8.25 - 10.31: 4 Bond angle restraints: 23847 Sorted by residual: angle pdb=" C ASN H 51 " pdb=" N THR H 52 " pdb=" CA THR H 52 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CA THR E 28 " pdb=" CB THR E 28 " pdb=" CG2 THR E 28 " ideal model delta sigma weight residual 110.50 117.29 -6.79 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CA THR G 28 " pdb=" CB THR G 28 " pdb=" CG2 THR G 28 " ideal model delta sigma weight residual 110.50 117.24 -6.74 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CB LYS C 365 " pdb=" CG LYS C 365 " pdb=" CD LYS C 365 " ideal model delta sigma weight residual 111.30 120.37 -9.07 2.30e+00 1.89e-01 1.55e+01 angle pdb=" CA THR D 28 " pdb=" CB THR D 28 " pdb=" CG2 THR D 28 " ideal model delta sigma weight residual 110.50 117.19 -6.69 1.70e+00 3.46e-01 1.55e+01 ... (remaining 23842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 9263 17.12 - 34.24: 822 34.24 - 51.36: 139 51.36 - 68.48: 21 68.48 - 85.60: 21 Dihedral angle restraints: 10266 sinusoidal: 4065 harmonic: 6201 Sorted by residual: dihedral pdb=" CA TYR B 178 " pdb=" C TYR B 178 " pdb=" N TYR B 179 " pdb=" CA TYR B 179 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA TYR A 178 " pdb=" C TYR A 178 " pdb=" N TYR A 179 " pdb=" CA TYR A 179 " ideal model delta harmonic sigma weight residual 180.00 140.79 39.21 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA TYR C 178 " pdb=" C TYR C 178 " pdb=" N TYR C 179 " pdb=" CA TYR C 179 " ideal model delta harmonic sigma weight residual 180.00 142.28 37.72 0 5.00e+00 4.00e-02 5.69e+01 ... (remaining 10263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1982 0.053 - 0.106: 448 0.106 - 0.159: 127 0.159 - 0.212: 15 0.212 - 0.265: 8 Chirality restraints: 2580 Sorted by residual: chirality pdb=" CB THR B 83 " pdb=" CA THR B 83 " pdb=" OG1 THR B 83 " pdb=" CG2 THR B 83 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR C 83 " pdb=" CA THR C 83 " pdb=" OG1 THR C 83 " pdb=" CG2 THR C 83 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB THR D 28 " pdb=" CA THR D 28 " pdb=" OG1 THR D 28 " pdb=" CG2 THR D 28 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2577 not shown) Planarity restraints: 3093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 159 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO C 160 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR L 33 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO L 34 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO L 34 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 34 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 33 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO H 34 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.038 5.00e-02 4.00e+02 ... (remaining 3090 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4690 2.82 - 3.34: 14329 3.34 - 3.86: 28747 3.86 - 4.38: 33455 4.38 - 4.90: 58627 Nonbonded interactions: 139848 Sorted by model distance: nonbonded pdb=" O TYR F 50 " pdb=" OG SER F 54 " model vdw 2.296 3.040 nonbonded pdb=" O PHE G 29 " pdb=" NH2 ARG G 72 " model vdw 2.309 3.120 nonbonded pdb=" O TYR C 142 " pdb=" OH TYR C 155 " model vdw 2.321 3.040 nonbonded pdb=" O GLU A 181 " pdb=" NE1 TRP A 487 " model vdw 2.322 3.120 nonbonded pdb=" OE1 GLU L 6 " pdb=" OG1 THR L 20 " model vdw 2.325 3.040 ... (remaining 139843 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' 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: 1.030 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.560 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.004 0.052 17514 Z= 0.174 Angle : 0.765 10.312 23859 Z= 0.406 Chirality : 0.052 0.265 2580 Planarity : 0.006 0.076 3093 Dihedral : 13.546 85.597 6288 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.17), residues: 2127 helix: -2.63 (0.32), residues: 132 sheet: -1.06 (0.17), residues: 855 loop : -1.04 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 192 TYR 0.031 0.002 TYR A 182 PHE 0.017 0.001 PHE C 508 TRP 0.027 0.001 TRP C 487 HIS 0.003 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00371 (17508) covalent geometry : angle 0.76479 (23847) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.93331 ( 12) hydrogen bonds : bond 0.14168 ( 396) hydrogen bonds : angle 7.72811 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 ARG cc_start: 0.7517 (ptp90) cc_final: 0.7233 (ptp90) REVERT: L 6 GLU cc_start: 0.7807 (pm20) cc_final: 0.7575 (pm20) REVERT: A 192 ARG cc_start: 0.7416 (ptp90) cc_final: 0.7135 (ptp90) REVERT: A 313 SER cc_start: 0.9212 (p) cc_final: 0.8980 (p) REVERT: A 498 MET cc_start: 0.6359 (mmp) cc_final: 0.5806 (mmp) REVERT: A 581 MET cc_start: 0.8850 (ptm) cc_final: 0.8548 (ptp) REVERT: C 202 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7271 (tt0) REVERT: C 203 TYR cc_start: 0.7850 (p90) cc_final: 0.7497 (p90) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1419 time to fit residues: 54.8391 Evaluate side-chains 212 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.5450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS B 409 ASN L 51 ASN A 415 ASN C 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.172539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145215 restraints weight = 20013.132| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.53 r_work: 0.3248 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17514 Z= 0.106 Angle : 0.555 11.069 23859 Z= 0.282 Chirality : 0.044 0.191 2580 Planarity : 0.005 0.067 3093 Dihedral : 4.789 36.759 2343 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.02 % Allowed : 7.01 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2127 helix: -1.66 (0.37), residues: 135 sheet: -0.95 (0.17), residues: 870 loop : -0.72 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 61 TYR 0.021 0.001 TYR B 465 PHE 0.014 0.001 PHE A 467 TRP 0.016 0.001 TRP C 487 HIS 0.002 0.000 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00240 (17508) covalent geometry : angle 0.55493 (23847) SS BOND : bond 0.00093 ( 6) SS BOND : angle 0.51800 ( 12) hydrogen bonds : bond 0.03116 ( 396) hydrogen bonds : angle 6.32516 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8688 (m-40) cc_final: 0.8456 (m110) REVERT: G 90 ASP cc_start: 0.8678 (m-30) cc_final: 0.8189 (t0) REVERT: A 192 ARG cc_start: 0.7339 (ptp90) cc_final: 0.7033 (ptp90) REVERT: A 581 MET cc_start: 0.8882 (ptm) cc_final: 0.8611 (ptp) REVERT: D 87 ARG cc_start: 0.7463 (mmt-90) cc_final: 0.7056 (mmp80) REVERT: C 202 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7733 (tm-30) outliers start: 19 outliers final: 15 residues processed: 239 average time/residue: 0.1453 time to fit residues: 52.0427 Evaluate side-chains 223 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 246 HIS L 39 GLN L 47 GLN A 102 HIS F 47 GLN C 409 ASN E 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113241 restraints weight = 20968.453| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.64 r_work: 0.2952 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17514 Z= 0.272 Angle : 0.680 9.945 23859 Z= 0.350 Chirality : 0.048 0.165 2580 Planarity : 0.005 0.075 3093 Dihedral : 5.214 38.604 2343 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.87 % Allowed : 10.27 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.18), residues: 2127 helix: -1.93 (0.35), residues: 135 sheet: -1.21 (0.17), residues: 873 loop : -0.79 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 61 TYR 0.021 0.002 TYR B 614 PHE 0.017 0.002 PHE A 393 TRP 0.017 0.001 TRP E 100 HIS 0.007 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00649 (17508) covalent geometry : angle 0.68040 (23847) SS BOND : bond 0.00553 ( 6) SS BOND : angle 0.49910 ( 12) hydrogen bonds : bond 0.03568 ( 396) hydrogen bonds : angle 6.49681 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 614 TYR cc_start: 0.7514 (t80) cc_final: 0.7294 (t80) REVERT: G 90 ASP cc_start: 0.8899 (m-30) cc_final: 0.8541 (t0) REVERT: A 192 ARG cc_start: 0.7523 (ptp90) cc_final: 0.7256 (ptp90) REVERT: A 614 TYR cc_start: 0.7289 (t80) cc_final: 0.7084 (t80) REVERT: D 87 ARG cc_start: 0.7346 (mmt-90) cc_final: 0.6984 (mmp80) REVERT: C 202 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 90 ASP cc_start: 0.8552 (t0) cc_final: 0.8163 (t0) outliers start: 35 outliers final: 23 residues processed: 245 average time/residue: 0.1418 time to fit residues: 52.1889 Evaluate side-chains 221 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 137 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 151 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS B 509 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119183 restraints weight = 20607.409| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.32 r_work: 0.3065 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17514 Z= 0.109 Angle : 0.550 12.103 23859 Z= 0.280 Chirality : 0.044 0.137 2580 Planarity : 0.004 0.071 3093 Dihedral : 4.792 35.360 2343 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.77 % Allowed : 12.84 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.18), residues: 2127 helix: -1.14 (0.43), residues: 114 sheet: -1.10 (0.17), residues: 870 loop : -0.57 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 212 TYR 0.027 0.001 TYR B 465 PHE 0.012 0.001 PHE D 29 TRP 0.012 0.001 TRP C 487 HIS 0.002 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00251 (17508) covalent geometry : angle 0.55047 (23847) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.33896 ( 12) hydrogen bonds : bond 0.02727 ( 396) hydrogen bonds : angle 6.07363 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8969 (m-30) cc_final: 0.8373 (t0) REVERT: A 192 ARG cc_start: 0.7368 (ptp90) cc_final: 0.7167 (ptp90) REVERT: D 38 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8218 (ttm170) REVERT: D 87 ARG cc_start: 0.7259 (mmt-90) cc_final: 0.6940 (mmp80) REVERT: C 202 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7689 (tm-30) REVERT: E 90 ASP cc_start: 0.8606 (t0) cc_final: 0.8104 (t0) outliers start: 33 outliers final: 22 residues processed: 238 average time/residue: 0.1392 time to fit residues: 49.9877 Evaluate side-chains 220 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS B 509 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 135 GLN C 409 ASN C 509 GLN H 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109734 restraints weight = 20930.903| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.63 r_work: 0.2913 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17514 Z= 0.302 Angle : 0.680 10.758 23859 Z= 0.350 Chirality : 0.048 0.188 2580 Planarity : 0.005 0.071 3093 Dihedral : 5.223 36.596 2343 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.68 % Allowed : 13.54 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 2127 helix: -1.61 (0.41), residues: 117 sheet: -1.33 (0.17), residues: 873 loop : -0.72 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 212 TYR 0.023 0.002 TYR B 465 PHE 0.019 0.002 PHE D 29 TRP 0.014 0.001 TRP E 100 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00719 (17508) covalent geometry : angle 0.68009 (23847) SS BOND : bond 0.00666 ( 6) SS BOND : angle 0.60876 ( 12) hydrogen bonds : bond 0.03439 ( 396) hydrogen bonds : angle 6.38053 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 PHE cc_start: 0.8971 (m-10) cc_final: 0.8769 (m-10) REVERT: G 90 ASP cc_start: 0.8931 (m-30) cc_final: 0.8408 (t0) REVERT: D 87 ARG cc_start: 0.7478 (mmt-90) cc_final: 0.7104 (mmp80) REVERT: C 202 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 510 ASP cc_start: 0.7489 (t0) cc_final: 0.7216 (t0) REVERT: E 38 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8461 (ttm170) REVERT: E 90 ASP cc_start: 0.8817 (t0) cc_final: 0.8121 (t0) outliers start: 50 outliers final: 34 residues processed: 246 average time/residue: 0.1406 time to fit residues: 52.3150 Evaluate side-chains 238 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 166 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN A 364 GLN A 439 HIS H 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.154647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114633 restraints weight = 20471.801| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.42 r_work: 0.3022 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17514 Z= 0.127 Angle : 0.564 12.043 23859 Z= 0.288 Chirality : 0.044 0.153 2580 Planarity : 0.004 0.073 3093 Dihedral : 4.858 34.018 2343 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.03 % Allowed : 14.66 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2127 helix: -0.98 (0.45), residues: 114 sheet: -1.26 (0.18), residues: 849 loop : -0.59 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 212 TYR 0.030 0.001 TYR B 465 PHE 0.014 0.001 PHE D 29 TRP 0.012 0.001 TRP A 487 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00296 (17508) covalent geometry : angle 0.56402 (23847) SS BOND : bond 0.00239 ( 6) SS BOND : angle 0.28420 ( 12) hydrogen bonds : bond 0.02762 ( 396) hydrogen bonds : angle 6.06214 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8887 (m-30) cc_final: 0.8450 (t0) REVERT: D 87 ARG cc_start: 0.7348 (mmt-90) cc_final: 0.6984 (mmp80) REVERT: C 202 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7650 (tm-30) REVERT: E 38 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8408 (ttm170) REVERT: E 90 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.7948 (t0) outliers start: 38 outliers final: 27 residues processed: 234 average time/residue: 0.1435 time to fit residues: 50.5821 Evaluate side-chains 230 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 6 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN C 135 GLN H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114496 restraints weight = 20728.706| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.65 r_work: 0.3004 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17514 Z= 0.156 Angle : 0.577 12.052 23859 Z= 0.293 Chirality : 0.044 0.176 2580 Planarity : 0.004 0.072 3093 Dihedral : 4.786 33.762 2343 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.30 % Allowed : 14.55 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.18), residues: 2127 helix: -0.99 (0.45), residues: 114 sheet: -1.23 (0.17), residues: 864 loop : -0.54 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 212 TYR 0.028 0.001 TYR B 465 PHE 0.014 0.001 PHE D 29 TRP 0.011 0.001 TRP L 23 HIS 0.003 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00367 (17508) covalent geometry : angle 0.57749 (23847) SS BOND : bond 0.00327 ( 6) SS BOND : angle 0.35572 ( 12) hydrogen bonds : bond 0.02864 ( 396) hydrogen bonds : angle 6.01680 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7975 (tm-30) REVERT: G 90 ASP cc_start: 0.8921 (m-30) cc_final: 0.8482 (t0) REVERT: D 87 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.6952 (mmp80) REVERT: C 202 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7649 (tm-30) REVERT: E 90 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8004 (t0) outliers start: 43 outliers final: 32 residues processed: 238 average time/residue: 0.1370 time to fit residues: 49.3600 Evaluate side-chains 237 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN F 5 GLN H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112414 restraints weight = 20737.969| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.66 r_work: 0.2932 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17514 Z= 0.242 Angle : 0.645 11.396 23859 Z= 0.329 Chirality : 0.046 0.202 2580 Planarity : 0.005 0.070 3093 Dihedral : 5.083 34.520 2343 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.14 % Allowed : 15.30 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 2127 helix: -1.24 (0.44), residues: 114 sheet: -1.37 (0.17), residues: 867 loop : -0.61 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 212 TYR 0.026 0.002 TYR A 614 PHE 0.016 0.001 PHE D 29 TRP 0.016 0.001 TRP E 100 HIS 0.004 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00574 (17508) covalent geometry : angle 0.64544 (23847) SS BOND : bond 0.00541 ( 6) SS BOND : angle 0.54550 ( 12) hydrogen bonds : bond 0.03187 ( 396) hydrogen bonds : angle 6.20584 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7925 (tm-30) REVERT: G 90 ASP cc_start: 0.8916 (m-30) cc_final: 0.8489 (t0) REVERT: D 87 ARG cc_start: 0.7440 (mmt-90) cc_final: 0.7004 (mmp80) REVERT: D 90 ASP cc_start: 0.8976 (t0) cc_final: 0.8132 (t0) REVERT: C 202 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 307 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8820 (ptm160) REVERT: E 90 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8205 (t0) outliers start: 40 outliers final: 34 residues processed: 236 average time/residue: 0.1460 time to fit residues: 51.3723 Evaluate side-chains 237 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 144 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN H 47 GLN H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118606 restraints weight = 20628.645| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.29 r_work: 0.3051 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17514 Z= 0.118 Angle : 0.559 12.367 23859 Z= 0.284 Chirality : 0.044 0.173 2580 Planarity : 0.004 0.073 3093 Dihedral : 4.745 33.661 2343 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.98 % Allowed : 15.68 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2127 helix: -0.78 (0.46), residues: 114 sheet: -1.24 (0.17), residues: 864 loop : -0.50 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 212 TYR 0.026 0.001 TYR A 614 PHE 0.013 0.001 PHE D 29 TRP 0.015 0.001 TRP B 487 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00272 (17508) covalent geometry : angle 0.55912 (23847) SS BOND : bond 0.00226 ( 6) SS BOND : angle 0.21615 ( 12) hydrogen bonds : bond 0.02634 ( 396) hydrogen bonds : angle 5.92757 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7887 (tt0) REVERT: B 576 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6792 (t0) REVERT: G 90 ASP cc_start: 0.8830 (m-30) cc_final: 0.8417 (t0) REVERT: D 87 ARG cc_start: 0.7336 (mmt-90) cc_final: 0.6926 (mmp80) REVERT: D 90 ASP cc_start: 0.8893 (t0) cc_final: 0.7670 (t0) REVERT: C 76 LYS cc_start: 0.8563 (mttm) cc_final: 0.8272 (mttm) REVERT: C 202 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7599 (tm-30) REVERT: C 365 LYS cc_start: 0.8511 (pttm) cc_final: 0.7881 (tppt) REVERT: E 90 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8139 (t0) outliers start: 37 outliers final: 31 residues processed: 236 average time/residue: 0.1374 time to fit residues: 49.1135 Evaluate side-chains 234 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 147 optimal weight: 0.0670 chunk 116 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 169 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN H 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118427 restraints weight = 20392.626| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.37 r_work: 0.3055 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17514 Z= 0.113 Angle : 0.558 12.439 23859 Z= 0.283 Chirality : 0.044 0.201 2580 Planarity : 0.004 0.074 3093 Dihedral : 4.612 32.114 2343 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.03 % Allowed : 16.05 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2127 helix: -0.67 (0.47), residues: 114 sheet: -1.15 (0.18), residues: 864 loop : -0.42 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 57 TYR 0.033 0.001 TYR A 614 PHE 0.012 0.001 PHE D 29 TRP 0.014 0.001 TRP L 23 HIS 0.002 0.000 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00261 (17508) covalent geometry : angle 0.55840 (23847) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.30605 ( 12) hydrogen bonds : bond 0.02668 ( 396) hydrogen bonds : angle 5.82350 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 TYR cc_start: 0.8709 (m-10) cc_final: 0.8508 (m-10) REVERT: B 202 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7862 (tt0) REVERT: G 90 ASP cc_start: 0.8798 (m-30) cc_final: 0.8450 (t0) REVERT: D 87 ARG cc_start: 0.7312 (mmt-90) cc_final: 0.7044 (mmp80) REVERT: D 90 ASP cc_start: 0.8877 (t0) cc_final: 0.7685 (t0) REVERT: C 76 LYS cc_start: 0.8557 (mttm) cc_final: 0.8291 (mttm) REVERT: C 202 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 90 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8110 (t0) outliers start: 38 outliers final: 27 residues processed: 240 average time/residue: 0.1414 time to fit residues: 50.7950 Evaluate side-chains 228 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN C 135 GLN H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117807 restraints weight = 20567.344| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.45 r_work: 0.3037 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17514 Z= 0.127 Angle : 0.566 12.472 23859 Z= 0.287 Chirality : 0.044 0.213 2580 Planarity : 0.004 0.072 3093 Dihedral : 4.584 31.822 2343 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.87 % Allowed : 16.05 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2127 helix: -0.79 (0.46), residues: 117 sheet: -1.13 (0.18), residues: 870 loop : -0.44 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 57 TYR 0.038 0.001 TYR A 614 PHE 0.012 0.001 PHE D 29 TRP 0.014 0.001 TRP L 23 HIS 0.002 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00299 (17508) covalent geometry : angle 0.56577 (23847) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.30520 ( 12) hydrogen bonds : bond 0.02715 ( 396) hydrogen bonds : angle 5.79043 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4413.20 seconds wall clock time: 76 minutes 26.03 seconds (4586.03 seconds total)