Starting phenix.real_space_refine on Mon Oct 14 05:44:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3p_38894/10_2024/8y3p_38894.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3p_38894/10_2024/8y3p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3p_38894/10_2024/8y3p_38894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3p_38894/10_2024/8y3p_38894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3p_38894/10_2024/8y3p_38894.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3p_38894/10_2024/8y3p_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 9.71, per 1000 atoms: 0.57 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: 3.99 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: 5.69 Time building geometry restraints manager: 4.61 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.940 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- 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 17508 Z= 0.246 Angle : 0.765 10.312 23847 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.875 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: 0.3226 time to fit residues: 125.1728 Evaluate side-chains 212 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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: 0.0070 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17508 Z= 0.153 Angle : 0.551 11.862 23847 Z= 0.280 Chirality : 0.044 0.189 2580 Planarity : 0.005 0.066 3093 Dihedral : 4.744 35.952 2343 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.96 % Allowed : 6.74 % Favored : 92.30 % 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: -1.39 (0.18), residues: 2127 helix: -1.62 (0.37), residues: 135 sheet: -0.92 (0.17), residues: 870 loop : -0.70 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 487 HIS 0.002 0.000 HIS A 488 PHE 0.014 0.001 PHE A 467 TYR 0.022 0.001 TYR B 465 ARG 0.005 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8587 (m-40) cc_final: 0.8349 (m110) REVERT: B 562 ILE cc_start: 0.8552 (mt) cc_final: 0.8347 (mt) REVERT: G 90 ASP cc_start: 0.8299 (m-30) cc_final: 0.8030 (t0) REVERT: A 192 ARG cc_start: 0.7404 (ptp90) cc_final: 0.7131 (ptp90) REVERT: A 581 MET cc_start: 0.8926 (ptm) cc_final: 0.8550 (ptp) REVERT: C 562 ILE cc_start: 0.8598 (mt) cc_final: 0.8372 (mt) REVERT: E 30 SER cc_start: 0.8472 (t) cc_final: 0.8272 (t) outliers start: 18 outliers final: 14 residues processed: 240 average time/residue: 0.3153 time to fit residues: 113.0553 Evaluate side-chains 219 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 105 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 170 optimal weight: 40.0000 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN A 102 HIS D 39 GLN F 47 GLN C 409 ASN E 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17508 Z= 0.298 Angle : 0.601 10.716 23847 Z= 0.307 Chirality : 0.045 0.174 2580 Planarity : 0.005 0.072 3093 Dihedral : 4.847 36.082 2343 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.98 % Allowed : 8.99 % Favored : 89.03 % 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: -1.44 (0.18), residues: 2127 helix: -1.62 (0.37), residues: 132 sheet: -1.01 (0.17), residues: 870 loop : -0.68 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 100 HIS 0.006 0.001 HIS A 488 PHE 0.013 0.001 PHE C 508 TYR 0.020 0.002 TYR A 614 ARG 0.005 0.000 ARG G 38 *********************** 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 253 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 216 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8309 (m-30) cc_final: 0.7708 (t0) REVERT: A 192 ARG cc_start: 0.7499 (ptp90) cc_final: 0.7214 (ptp90) REVERT: A 581 MET cc_start: 0.8995 (ptm) cc_final: 0.8723 (ptp) REVERT: D 106 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7762 (tt) REVERT: C 202 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7531 (tm-30) REVERT: E 90 ASP cc_start: 0.8082 (t0) cc_final: 0.7866 (t0) outliers start: 37 outliers final: 27 residues processed: 241 average time/residue: 0.3152 time to fit residues: 115.0813 Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 B residue 524 ASP Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 LEU 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 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 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 188 optimal weight: 0.0980 chunk 143 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 B 509 GLN L 47 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17508 Z= 0.383 Angle : 0.640 10.767 23847 Z= 0.328 Chirality : 0.046 0.149 2580 Planarity : 0.005 0.075 3093 Dihedral : 5.097 36.690 2343 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.25 % Allowed : 11.66 % Favored : 86.09 % 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: -1.61 (0.18), residues: 2127 helix: -1.61 (0.38), residues: 132 sheet: -1.19 (0.17), residues: 873 loop : -0.76 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 100 HIS 0.006 0.001 HIS A 488 PHE 0.013 0.001 PHE A 393 TYR 0.024 0.002 TYR B 465 ARG 0.009 0.001 ARG A 212 *********************** 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 257 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.7535 (ptp90) cc_final: 0.7263 (ptp90) REVERT: C 202 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7602 (tm-30) REVERT: E 90 ASP cc_start: 0.8280 (t0) cc_final: 0.7822 (t0) outliers start: 42 outliers final: 32 residues processed: 243 average time/residue: 0.3027 time to fit residues: 110.5757 Evaluate side-chains 232 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR 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 B residue 524 ASP 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 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 405 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 159 ASP 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 69 THR 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 169 optimal weight: 30.0000 chunk 115 optimal weight: 0.0770 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 chunk 182 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS A 364 GLN C 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17508 Z= 0.166 Angle : 0.544 12.176 23847 Z= 0.278 Chirality : 0.044 0.144 2580 Planarity : 0.004 0.071 3093 Dihedral : 4.738 33.524 2343 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.93 % Allowed : 13.06 % Favored : 85.02 % 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: -1.33 (0.18), residues: 2127 helix: -1.06 (0.44), residues: 114 sheet: -1.07 (0.18), residues: 855 loop : -0.58 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.004 0.001 HIS A 488 PHE 0.013 0.001 PHE D 29 TYR 0.028 0.001 TYR B 465 ARG 0.006 0.000 ARG C 485 *********************** 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 258 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8327 (t0) cc_final: 0.7833 (t0) REVERT: L 104 THR cc_start: 0.8516 (m) cc_final: 0.8315 (m) REVERT: C 202 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7485 (tm-30) REVERT: E 90 ASP cc_start: 0.8207 (t0) cc_final: 0.7688 (t0) outliers start: 36 outliers final: 23 residues processed: 246 average time/residue: 0.3025 time to fit residues: 111.5218 Evaluate side-chains 224 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 2.058 ------------------------------------------------------------------------------- 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 524 ASP Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 159 ASP 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 E residue 89 GLU Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.7980 chunk 182 optimal weight: 0.0870 chunk 40 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN C 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17508 Z= 0.206 Angle : 0.553 12.279 23847 Z= 0.281 Chirality : 0.044 0.169 2580 Planarity : 0.004 0.072 3093 Dihedral : 4.641 33.921 2343 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.03 % Allowed : 14.02 % Favored : 83.95 % 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: -1.23 (0.18), residues: 2127 helix: -0.96 (0.45), residues: 114 sheet: -1.03 (0.18), residues: 849 loop : -0.49 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 23 HIS 0.004 0.001 HIS B 488 PHE 0.014 0.001 PHE D 29 TYR 0.029 0.001 TYR B 465 ARG 0.005 0.000 ARG A 212 *********************** 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 248 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7875 (t0) REVERT: D 90 ASP cc_start: 0.7992 (t0) cc_final: 0.7711 (t0) REVERT: C 202 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 90 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7728 (t0) outliers start: 38 outliers final: 29 residues processed: 235 average time/residue: 0.2975 time to fit residues: 105.0462 Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain 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 159 ASP 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 242 LEU 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 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 113 optimal weight: 0.0970 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN A 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17508 Z= 0.328 Angle : 0.612 11.658 23847 Z= 0.312 Chirality : 0.045 0.193 2580 Planarity : 0.005 0.071 3093 Dihedral : 4.877 34.803 2343 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.46 % Allowed : 14.45 % Favored : 83.09 % 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: -1.38 (0.18), residues: 2127 helix: -1.26 (0.43), residues: 114 sheet: -1.12 (0.17), residues: 870 loop : -0.57 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 100 HIS 0.005 0.001 HIS B 488 PHE 0.015 0.001 PHE D 29 TYR 0.027 0.002 TYR B 465 ARG 0.007 0.001 ARG B 212 *********************** 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 260 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7719 (tm-30) REVERT: G 90 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7901 (t0) REVERT: D 90 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7169 (t0) REVERT: C 202 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7578 (tm-30) REVERT: E 90 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7833 (t0) outliers start: 46 outliers final: 32 residues processed: 243 average time/residue: 0.3048 time to fit residues: 111.8437 Evaluate side-chains 238 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 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 D residue 30 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 90 ASP 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 232 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN C 246 HIS H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17508 Z= 0.178 Angle : 0.551 12.297 23847 Z= 0.279 Chirality : 0.044 0.176 2580 Planarity : 0.004 0.072 3093 Dihedral : 4.621 32.349 2343 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.51 % Allowed : 14.50 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.25 (0.18), residues: 2127 helix: -0.86 (0.46), residues: 114 sheet: -1.09 (0.18), residues: 855 loop : -0.48 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 100 HIS 0.003 0.001 HIS B 246 PHE 0.012 0.001 PHE D 29 TYR 0.028 0.001 TYR B 465 ARG 0.006 0.000 ARG C 307 *********************** 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 261 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 214 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7475 (tt0) REVERT: G 90 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7924 (t0) REVERT: D 43 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7479 (mtmm) REVERT: D 90 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7707 (t0) REVERT: D 106 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7739 (tt) REVERT: C 202 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7427 (tm-30) REVERT: E 90 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7729 (t0) outliers start: 47 outliers final: 35 residues processed: 245 average time/residue: 0.3022 time to fit residues: 112.5100 Evaluate side-chains 244 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 205 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 LEU 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 232 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 477 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.0770 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 30.0000 chunk 178 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN A 509 GLN D 82 GLN C 246 HIS H 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17508 Z= 0.281 Angle : 0.596 12.100 23847 Z= 0.302 Chirality : 0.045 0.200 2580 Planarity : 0.004 0.071 3093 Dihedral : 4.747 33.656 2343 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.46 % Allowed : 14.61 % 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: -1.33 (0.18), residues: 2127 helix: -1.14 (0.45), residues: 114 sheet: -1.14 (0.18), residues: 852 loop : -0.51 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 100 HIS 0.005 0.001 HIS C 488 PHE 0.014 0.001 PHE D 29 TYR 0.026 0.001 TYR B 465 ARG 0.007 0.001 ARG B 212 *********************** 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 259 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 213 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7642 (tm-30) REVERT: G 90 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7910 (t0) REVERT: G 106 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7805 (tt) REVERT: D 90 ASP cc_start: 0.8439 (t0) cc_final: 0.7768 (t0) REVERT: D 106 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7801 (tt) REVERT: C 202 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7489 (tm-30) REVERT: E 90 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7793 (t0) REVERT: H 10 SER cc_start: 0.8564 (m) cc_final: 0.7984 (t) outliers start: 46 outliers final: 36 residues processed: 241 average time/residue: 0.3000 time to fit residues: 111.3947 Evaluate side-chains 249 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 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 D residue 89 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 LEU 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 35 ASN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 138 optimal weight: 0.6980 chunk 209 optimal weight: 0.3980 chunk 192 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 0.0770 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN C 135 GLN H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17508 Z= 0.151 Angle : 0.543 12.906 23847 Z= 0.275 Chirality : 0.044 0.194 2580 Planarity : 0.004 0.073 3093 Dihedral : 4.485 30.743 2343 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.93 % Allowed : 15.41 % Favored : 82.66 % 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: -1.15 (0.18), residues: 2127 helix: -0.68 (0.46), residues: 114 sheet: -1.01 (0.18), residues: 852 loop : -0.43 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 23 HIS 0.003 0.000 HIS B 246 PHE 0.011 0.001 PHE B 101 TYR 0.025 0.001 TYR B 465 ARG 0.006 0.000 ARG B 212 ********************** 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 251 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7425 (tt0) REVERT: G 43 LYS cc_start: 0.7678 (mmtm) cc_final: 0.7473 (mtmm) REVERT: G 90 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7890 (t0) REVERT: D 90 ASP cc_start: 0.8433 (t0) cc_final: 0.7358 (t0) REVERT: C 202 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7343 (tm-30) REVERT: E 90 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7699 (t0) REVERT: H 10 SER cc_start: 0.8242 (m) cc_final: 0.7633 (t) outliers start: 36 outliers final: 26 residues processed: 238 average time/residue: 0.3109 time to fit residues: 111.2604 Evaluate side-chains 233 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 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 F residue 29 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 171 optimal weight: 5.9990 chunk 21 optimal weight: 0.1980 chunk 30 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN F 5 GLN H 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118633 restraints weight = 20572.728| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.45 r_work: 0.3056 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17508 Z= 0.219 Angle : 0.569 12.594 23847 Z= 0.286 Chirality : 0.045 0.224 2580 Planarity : 0.004 0.073 3093 Dihedral : 4.529 31.746 2343 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.77 % Allowed : 15.62 % Favored : 82.61 % 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: -1.17 (0.18), residues: 2127 helix: -0.80 (0.46), residues: 114 sheet: -1.00 (0.18), residues: 855 loop : -0.45 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 100 HIS 0.003 0.001 HIS C 488 PHE 0.012 0.001 PHE D 29 TYR 0.034 0.001 TYR A 614 ARG 0.007 0.000 ARG D 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.18 seconds wall clock time: 66 minutes 23.51 seconds (3983.51 seconds total)