Starting phenix.real_space_refine on Sun Jun 15 04:15:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3p_38894/06_2025/8y3p_38894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3p_38894/06_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_38894/06_2025/8y3p_38894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3p_38894/06_2025/8y3p_38894.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3p_38894/06_2025/8y3p_38894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3p_38894/06_2025/8y3p_38894.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.29, per 1000 atoms: 0.60 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: 4.08 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.22 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: 5.63 Time building geometry restraints manager: 4.86 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: 0.01 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: 0.710 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.810 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (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 TRP 0.027 0.001 TRP C 487 HIS 0.003 0.001 HIS C 488 PHE 0.017 0.001 PHE C 508 TYR 0.031 0.002 TYR A 182 ARG 0.010 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.14168 ( 396) hydrogen bonds : angle 7.72811 ( 999) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.93331 ( 12) covalent geometry : bond 0.00371 (17508) covalent geometry : angle 0.76479 (23847) *********************** 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 : 1.961 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: 0.7574 (pm20) REVERT: A 192 ARG cc_start: 0.7416 (ptp90) cc_final: 0.7136 (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: 0.5805 (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: 0.7272 (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: 0.3027 time to fit residues: 117.4369 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 : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 0.0270 chunk 85 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 190 optimal weight: 0.0970 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.166662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127787 restraints weight = 20501.190| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.50 r_work: 0.3166 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17514 Z= 0.102 Angle : 0.552 11.467 23859 Z= 0.281 Chirality : 0.044 0.192 2580 Planarity : 0.005 0.066 3093 Dihedral : 4.774 36.391 2343 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.96 % Allowed : 6.90 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2127 helix: -1.62 (0.37), residues: 135 sheet: -0.92 (0.17), residues: 870 loop : -0.72 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 487 HIS 0.002 0.000 HIS B 488 PHE 0.014 0.001 PHE A 467 TYR 0.021 0.001 TYR B 465 ARG 0.005 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 396) hydrogen bonds : angle 6.32770 ( 999) SS BOND : bond 0.00094 ( 6) SS BOND : angle 0.54603 ( 12) covalent geometry : bond 0.00232 (17508) covalent geometry : angle 0.55165 (23847) *********************** 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 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8702 (m-40) cc_final: 0.8500 (m110) REVERT: G 90 ASP cc_start: 0.8796 (m-30) cc_final: 0.8305 (t0) REVERT: A 192 ARG cc_start: 0.7335 (ptp90) cc_final: 0.7036 (ptp90) REVERT: A 581 MET cc_start: 0.8945 (ptm) cc_final: 0.8645 (ptp) REVERT: D 87 ARG cc_start: 0.7520 (mmt-90) cc_final: 0.7045 (mmp80) REVERT: C 202 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 57 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8011 (ttt-90) outliers start: 18 outliers final: 14 residues processed: 238 average time/residue: 0.3080 time to fit residues: 109.7267 Evaluate side-chains 223 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 H residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 21 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 106 optimal weight: 0.0980 chunk 48 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 E 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115400 restraints weight = 20739.236| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.54 r_work: 0.2978 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17514 Z= 0.255 Angle : 0.663 10.319 23859 Z= 0.340 Chirality : 0.047 0.169 2580 Planarity : 0.005 0.074 3093 Dihedral : 5.133 37.815 2343 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.03 % Allowed : 9.68 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.18), residues: 2127 helix: -1.89 (0.35), residues: 135 sheet: -1.15 (0.17), residues: 873 loop : -0.77 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 100 HIS 0.007 0.001 HIS A 488 PHE 0.015 0.001 PHE C 508 TYR 0.021 0.002 TYR A 614 ARG 0.006 0.001 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 396) hydrogen bonds : angle 6.41769 ( 999) SS BOND : bond 0.00476 ( 6) SS BOND : angle 0.42874 ( 12) covalent geometry : bond 0.00606 (17508) covalent geometry : angle 0.66275 (23847) *********************** 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 260 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 614 TYR cc_start: 0.7428 (t80) cc_final: 0.7165 (t80) REVERT: G 90 ASP cc_start: 0.8882 (m-30) cc_final: 0.8378 (t0) REVERT: A 192 ARG cc_start: 0.7504 (ptp90) cc_final: 0.7230 (ptp90) REVERT: A 614 TYR cc_start: 0.7242 (t80) cc_final: 0.6994 (t80) REVERT: D 87 ARG cc_start: 0.7375 (mmt-90) cc_final: 0.7044 (mmp80) REVERT: C 202 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7807 (tm-30) REVERT: E 90 ASP cc_start: 0.8598 (t0) cc_final: 0.8070 (t0) outliers start: 38 outliers final: 26 residues processed: 248 average time/residue: 0.2992 time to fit residues: 112.0625 Evaluate side-chains 223 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 2.050 ------------------------------------------------------------------------------- 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 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 A residue 532 ILE 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 58 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN C 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116245 restraints weight = 20582.692| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.58 r_work: 0.3002 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17514 Z= 0.170 Angle : 0.590 11.414 23859 Z= 0.300 Chirality : 0.045 0.142 2580 Planarity : 0.005 0.073 3093 Dihedral : 4.952 35.515 2343 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.93 % Allowed : 12.63 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2127 helix: -1.54 (0.40), residues: 117 sheet: -1.17 (0.17), residues: 870 loop : -0.66 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 100 HIS 0.004 0.001 HIS A 488 PHE 0.015 0.001 PHE D 29 TYR 0.026 0.001 TYR B 465 ARG 0.007 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 396) hydrogen bonds : angle 6.19601 ( 999) SS BOND : bond 0.00354 ( 6) SS BOND : angle 0.28320 ( 12) covalent geometry : bond 0.00402 (17508) covalent geometry : angle 0.58989 (23847) *********************** 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 250 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 TYR cc_start: 0.8959 (m-80) cc_final: 0.8643 (m-10) REVERT: B 614 TYR cc_start: 0.7162 (t80) cc_final: 0.6893 (t80) REVERT: G 90 ASP cc_start: 0.8833 (m-30) cc_final: 0.8273 (t0) REVERT: L 6 GLU cc_start: 0.8659 (pm20) cc_final: 0.8396 (pt0) REVERT: A 192 ARG cc_start: 0.7474 (ptp90) cc_final: 0.7166 (ptp90) REVERT: A 614 TYR cc_start: 0.6991 (t80) cc_final: 0.6755 (t80) REVERT: D 87 ARG cc_start: 0.7346 (mmt-90) cc_final: 0.7026 (mmp80) REVERT: C 202 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7722 (tm-30) REVERT: E 90 ASP cc_start: 0.8685 (t0) cc_final: 0.8134 (t0) outliers start: 36 outliers final: 26 residues processed: 241 average time/residue: 0.3653 time to fit residues: 137.7375 Evaluate side-chains 226 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 3.063 ------------------------------------------------------------------------------- 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 85 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 526 SER Chi-restraints excluded: chain A residue 532 ILE 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 C residue 466 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 51 VAL 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 13 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 29 optimal weight: 40.0000 chunk 45 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 157 optimal weight: 0.2980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 C 102 HIS C 409 ASN C 509 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115238 restraints weight = 20890.759| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.70 r_work: 0.2990 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2200 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= 0.174 Angle : 0.586 11.493 23859 Z= 0.299 Chirality : 0.045 0.156 2580 Planarity : 0.005 0.073 3093 Dihedral : 4.877 34.282 2343 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.57 % Allowed : 13.43 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2127 helix: -1.37 (0.42), residues: 117 sheet: -1.20 (0.17), residues: 870 loop : -0.65 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 100 HIS 0.005 0.001 HIS A 488 PHE 0.014 0.001 PHE D 29 TYR 0.027 0.001 TYR B 465 ARG 0.006 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 396) hydrogen bonds : angle 6.10003 ( 999) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.31996 ( 12) covalent geometry : bond 0.00409 (17508) covalent geometry : angle 0.58643 (23847) *********************** 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 262 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 TYR cc_start: 0.8978 (m-80) cc_final: 0.8680 (m-10) REVERT: B 614 TYR cc_start: 0.7227 (t80) cc_final: 0.7018 (t80) REVERT: G 90 ASP cc_start: 0.8811 (m-30) cc_final: 0.8348 (t0) REVERT: G 106 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8008 (tt) REVERT: D 38 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (ttm170) REVERT: D 43 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7620 (mtmm) REVERT: D 87 ARG cc_start: 0.7413 (mmt-90) cc_final: 0.7089 (mmp80) REVERT: D 106 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7970 (tt) REVERT: C 202 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 614 TYR cc_start: 0.7211 (t80) cc_final: 0.6764 (t80) REVERT: E 90 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8062 (t0) outliers start: 48 outliers final: 35 residues processed: 245 average time/residue: 0.3547 time to fit residues: 133.3660 Evaluate side-chains 241 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 106 LEU Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 85 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 242 LEU 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 A residue 532 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 106 LEU 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 232 VAL 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 30 SER 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 E residue 90 ASP 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 43 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 152 optimal weight: 0.0070 chunk 124 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111457 restraints weight = 20940.580| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.54 r_work: 0.2937 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17514 Z= 0.244 Angle : 0.642 11.372 23859 Z= 0.328 Chirality : 0.046 0.175 2580 Planarity : 0.005 0.071 3093 Dihedral : 5.100 34.833 2343 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.73 % Allowed : 14.34 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 2127 helix: -1.35 (0.43), residues: 114 sheet: -1.37 (0.17), residues: 858 loop : -0.73 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 100 HIS 0.005 0.001 HIS A 488 PHE 0.017 0.001 PHE D 29 TYR 0.026 0.002 TYR B 465 ARG 0.010 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 396) hydrogen bonds : angle 6.21807 ( 999) SS BOND : bond 0.00525 ( 6) SS BOND : angle 0.45647 ( 12) covalent geometry : bond 0.00577 (17508) covalent geometry : angle 0.64169 (23847) *********************** 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 265 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8888 (m-30) cc_final: 0.8432 (t0) REVERT: G 106 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8081 (tt) REVERT: L 104 THR cc_start: 0.8887 (m) cc_final: 0.8674 (m) REVERT: D 38 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8221 (ttm170) REVERT: D 87 ARG cc_start: 0.7462 (mmt-90) cc_final: 0.7068 (mmp80) REVERT: C 202 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 307 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8876 (ptm160) REVERT: C 365 LYS cc_start: 0.8648 (pttm) cc_final: 0.8398 (pttm) REVERT: C 614 TYR cc_start: 0.7319 (t80) cc_final: 0.6990 (t80) REVERT: E 90 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8181 (t0) outliers start: 51 outliers final: 38 residues processed: 246 average time/residue: 0.3119 time to fit residues: 115.4243 Evaluate side-chains 248 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 85 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 242 LEU 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 A residue 532 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 29 THR 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 307 ARG Chi-restraints excluded: chain C residue 410 ASN 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 51 VAL 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 Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 205 optimal weight: 0.0370 chunk 208 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN C 409 ASN H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117672 restraints weight = 20619.797| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.84 r_work: 0.3017 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17514 Z= 0.113 Angle : 0.551 12.139 23859 Z= 0.281 Chirality : 0.044 0.161 2580 Planarity : 0.004 0.071 3093 Dihedral : 4.748 32.261 2343 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.41 % Allowed : 14.93 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2127 helix: -0.85 (0.46), residues: 114 sheet: -1.27 (0.17), residues: 864 loop : -0.62 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.002 0.000 HIS A 488 PHE 0.013 0.001 PHE D 29 TYR 0.030 0.001 TYR B 465 ARG 0.005 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.02646 ( 396) hydrogen bonds : angle 5.92216 ( 999) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.19879 ( 12) covalent geometry : bond 0.00257 (17508) covalent geometry : angle 0.55151 (23847) *********************** 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 262 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7772 (tm-30) REVERT: G 90 ASP cc_start: 0.8820 (m-30) cc_final: 0.8453 (t0) REVERT: G 106 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7907 (tt) REVERT: D 38 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8225 (ttm170) REVERT: D 87 ARG cc_start: 0.7459 (mmt-90) cc_final: 0.7138 (mmp80) REVERT: D 90 ASP cc_start: 0.8888 (t0) cc_final: 0.7778 (t0) REVERT: C 202 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7580 (tm-30) REVERT: E 90 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8108 (t0) outliers start: 45 outliers final: 35 residues processed: 248 average time/residue: 0.3917 time to fit residues: 149.3480 Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 85 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 242 LEU 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 A residue 532 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 6 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 222 THR Chi-restraints excluded: chain C residue 410 ASN 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 35 ASN 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 Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 134 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN D 39 GLN F 39 GLN C 135 GLN H 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112682 restraints weight = 20653.746| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.37 r_work: 0.2966 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17514 Z= 0.222 Angle : 0.626 11.612 23859 Z= 0.319 Chirality : 0.046 0.187 2580 Planarity : 0.005 0.070 3093 Dihedral : 4.972 33.940 2343 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.57 % Allowed : 15.25 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2127 helix: -1.17 (0.44), residues: 114 sheet: -1.35 (0.17), residues: 873 loop : -0.66 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 100 HIS 0.003 0.001 HIS B 488 PHE 0.016 0.001 PHE D 29 TYR 0.026 0.002 TYR A 614 ARG 0.007 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 396) hydrogen bonds : angle 6.10069 ( 999) SS BOND : bond 0.00507 ( 6) SS BOND : angle 0.50728 ( 12) covalent geometry : bond 0.00525 (17508) covalent geometry : angle 0.62619 (23847) *********************** 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 258 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7733 (tm-30) REVERT: G 90 ASP cc_start: 0.8880 (m-30) cc_final: 0.8484 (t0) REVERT: A 128 MET cc_start: 0.8922 (tpt) cc_final: 0.8685 (tpt) REVERT: D 38 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8270 (ttm170) REVERT: D 87 ARG cc_start: 0.7459 (mmt-90) cc_final: 0.7035 (mmp80) REVERT: C 202 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 90 ASP cc_start: 0.8822 (t0) cc_final: 0.8196 (t0) outliers start: 48 outliers final: 40 residues processed: 239 average time/residue: 0.2816 time to fit residues: 102.6750 Evaluate side-chains 248 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 85 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 242 LEU 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 A residue 532 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 6 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 410 ASN 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 35 ASN Chi-restraints excluded: chain E residue 58 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116503 restraints weight = 20661.312| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.65 r_work: 0.3017 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2505 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= 0.128 Angle : 0.567 11.981 23859 Z= 0.287 Chirality : 0.044 0.174 2580 Planarity : 0.004 0.072 3093 Dihedral : 4.755 32.149 2343 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.25 % Allowed : 15.25 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2127 helix: -0.88 (0.46), residues: 114 sheet: -1.28 (0.17), residues: 867 loop : -0.52 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 100 HIS 0.002 0.001 HIS C 488 PHE 0.013 0.001 PHE D 29 TYR 0.027 0.001 TYR B 465 ARG 0.005 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.02696 ( 396) hydrogen bonds : angle 5.90252 ( 999) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.22241 ( 12) covalent geometry : bond 0.00298 (17508) covalent geometry : angle 0.56669 (23847) *********************** 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 252 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8764 (m-30) cc_final: 0.8485 (t0) REVERT: L 6 GLU cc_start: 0.8378 (pm20) cc_final: 0.8177 (pt0) REVERT: A 128 MET cc_start: 0.8841 (tpt) cc_final: 0.8567 (tpt) REVERT: D 38 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8314 (ttm170) REVERT: D 87 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.7087 (mmp80) REVERT: D 90 ASP cc_start: 0.8882 (t0) cc_final: 0.7733 (t0) REVERT: C 76 LYS cc_start: 0.8565 (mttm) cc_final: 0.8362 (mttm) REVERT: C 202 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7592 (tm-30) REVERT: E 90 ASP cc_start: 0.8725 (t0) cc_final: 0.8108 (t0) outliers start: 42 outliers final: 35 residues processed: 241 average time/residue: 0.2852 time to fit residues: 103.9896 Evaluate side-chains 240 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 29 THR Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR 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 410 ASN Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 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 = 0.3769 r_free = 0.3769 target = 0.155893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117416 restraints weight = 20513.423| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.44 r_work: 0.3038 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17514 Z= 0.117 Angle : 0.560 12.466 23859 Z= 0.284 Chirality : 0.044 0.191 2580 Planarity : 0.004 0.072 3093 Dihedral : 4.649 31.667 2343 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.35 % Allowed : 15.36 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2127 helix: -0.72 (0.46), residues: 114 sheet: -1.21 (0.17), residues: 867 loop : -0.45 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.002 0.001 HIS B 107 PHE 0.013 0.001 PHE D 29 TYR 0.034 0.001 TYR A 614 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.02635 ( 396) hydrogen bonds : angle 5.80465 ( 999) SS BOND : bond 0.00223 ( 6) SS BOND : angle 0.26267 ( 12) covalent geometry : bond 0.00271 (17508) covalent geometry : angle 0.56057 (23847) ********************** 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 256 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7894 (tt0) REVERT: G 90 ASP cc_start: 0.8788 (m-30) cc_final: 0.8507 (t0) REVERT: L 6 GLU cc_start: 0.8474 (pm20) cc_final: 0.8199 (pt0) REVERT: D 38 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8283 (ttm170) REVERT: D 87 ARG cc_start: 0.7348 (mmt-90) cc_final: 0.7109 (mmp80) REVERT: D 90 ASP cc_start: 0.8845 (t0) cc_final: 0.7572 (t0) REVERT: C 76 LYS cc_start: 0.8559 (mttm) cc_final: 0.8353 (mttm) REVERT: C 202 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7592 (tm-30) REVERT: E 90 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8101 (t0) outliers start: 44 outliers final: 36 residues processed: 242 average time/residue: 0.3147 time to fit residues: 114.8092 Evaluate side-chains 242 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 29 THR Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 6 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 410 ASN Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 35 ASN 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 Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 0.6980 chunk 200 optimal weight: 0.0980 chunk 107 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119571 restraints weight = 20427.429| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.44 r_work: 0.3067 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17514 Z= 0.103 Angle : 0.548 12.887 23859 Z= 0.277 Chirality : 0.044 0.197 2580 Planarity : 0.004 0.072 3093 Dihedral : 4.522 30.649 2343 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.25 % Allowed : 15.52 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2127 helix: -0.55 (0.47), residues: 114 sheet: -1.14 (0.18), residues: 855 loop : -0.45 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 487 HIS 0.002 0.000 HIS B 107 PHE 0.012 0.001 PHE D 29 TYR 0.034 0.001 TYR A 614 ARG 0.005 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.02546 ( 396) hydrogen bonds : angle 5.70147 ( 999) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.23857 ( 12) covalent geometry : bond 0.00236 (17508) covalent geometry : angle 0.54828 (23847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9357.27 seconds wall clock time: 164 minutes 33.39 seconds (9873.39 seconds total)