Starting phenix.real_space_refine on Sun Jul 21 19:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0c_36760/07_2024/8k0c_36760.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0c_36760/07_2024/8k0c_36760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0c_36760/07_2024/8k0c_36760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0c_36760/07_2024/8k0c_36760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0c_36760/07_2024/8k0c_36760.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0c_36760/07_2024/8k0c_36760.cif" } resolution = 3.18 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= 0.010 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 70 5.16 5 C 9656 2.51 5 N 2550 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15262 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3749 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 450} Chain breaks: 1 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 420 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "G" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "H" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3749 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 450} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 420 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Time building chain proxies: 10.77, per 1000 atoms: 0.71 Number of scatterers: 15262 At special positions: 0 Unit cell: (168.1, 84.46, 174.66, 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 70 16.00 O 2986 8.00 N 2550 7.00 C 9656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.02 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.02 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS D 146 " distance=2.01 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.61 Conformation dependent library (CDL) restraints added in 2.9 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 14.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 118 through 146 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.815A pdb=" N GLN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.763A pdb=" N LEU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 118 through 146 removed outlier: 3.554A pdb=" N ALA C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'H' and resid 120 through 127 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 118 through 146 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.815A pdb=" N GLN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.763A pdb=" N LEU B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.554A pdb=" N ALA D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.860A pdb=" N VAL E 12 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 47 through 48 removed outlier: 3.559A pdb=" N ALA E 98 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 118 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR E 101 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE E 116 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR E 103 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASN E 114 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AA6, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AA7, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.593A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.687A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 153 through 154 removed outlier: 4.580A pdb=" N TRP F 147 " --> pdb=" O GLN F 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 579 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 579 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 217 through 222 removed outlier: 5.880A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 279 through 286 removed outlier: 5.602A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 313 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 316 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 347 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 356 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.562A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 468 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.555A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU G 82 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU G 82 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.860A pdb=" N VAL G 12 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 47 through 48 removed outlier: 3.559A pdb=" N ALA G 98 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL G 118 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR G 101 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE G 116 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR G 103 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASN G 114 " --> pdb=" O TYR G 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 136 through 140 Processing sheet with id=AC8, first strand: chain 'G' and resid 136 through 140 Processing sheet with id=AC9, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AD1, first strand: chain 'G' and resid 185 through 186 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER H 7 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.593A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 113 through 117 removed outlier: 3.687A pdb=" N ASN H 136 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR H 172 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 154 removed outlier: 4.580A pdb=" N TRP H 147 " --> pdb=" O GLN H 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 579 " --> pdb=" O LYS B 560 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 579 " --> pdb=" O LYS B 560 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 217 through 222 removed outlier: 5.880A pdb=" N SER B 232 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 222 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA B 230 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 279 through 286 removed outlier: 5.602A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 313 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 356 " --> pdb=" O TYR B 363 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.562A pdb=" N SER B 447 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.555A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1686 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: 5.45 Time building geometry restraints manager: 7.28 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: 4802 1.34 - 1.46: 3438 1.46 - 1.58: 7292 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 15620 Sorted by residual: bond pdb=" CD LYS A 465 " pdb=" CE LYS A 465 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.18e+00 bond pdb=" CD LYS B 465 " pdb=" CE LYS B 465 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.18e+00 bond pdb=" CB TYR B 291 " pdb=" CG TYR B 291 " ideal model delta sigma weight residual 1.512 1.468 0.044 2.20e-02 2.07e+03 4.05e+00 bond pdb=" CB TYR A 291 " pdb=" CG TYR A 291 " ideal model delta sigma weight residual 1.512 1.468 0.044 2.20e-02 2.07e+03 4.05e+00 bond pdb=" C SER B 486 " pdb=" N ARG B 487 " ideal model delta sigma weight residual 1.331 1.301 0.030 1.59e-02 3.96e+03 3.49e+00 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 96.74 - 104.38: 318 104.38 - 112.01: 7733 112.01 - 119.65: 5484 119.65 - 127.28: 7549 127.28 - 134.92: 186 Bond angle restraints: 21270 Sorted by residual: angle pdb=" C THR F 50 " pdb=" N ALA F 51 " pdb=" CA ALA F 51 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C THR H 50 " pdb=" N ALA H 51 " pdb=" CA ALA H 51 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C THR F 94 " pdb=" N PRO F 95 " pdb=" CA PRO F 95 " ideal model delta sigma weight residual 127.00 134.92 -7.92 2.40e+00 1.74e-01 1.09e+01 angle pdb=" C THR H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta sigma weight residual 127.00 134.92 -7.92 2.40e+00 1.74e-01 1.09e+01 angle pdb=" N LYS E 217 " pdb=" CA LYS E 217 " pdb=" C LYS E 217 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.89e+00 ... (remaining 21265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.83: 8980 14.83 - 29.66: 334 29.66 - 44.49: 92 44.49 - 59.32: 16 59.32 - 74.15: 6 Dihedral angle restraints: 9428 sinusoidal: 3682 harmonic: 5746 Sorted by residual: dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual 93.00 161.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS B 146 " pdb=" SG CYS B 146 " pdb=" SG CYS D 146 " pdb=" CB CYS D 146 " ideal model delta sinusoidal sigma weight residual 93.00 161.19 -68.19 1 1.00e+01 1.00e-02 6.03e+01 dihedral pdb=" CA GLY G 107 " pdb=" C GLY G 107 " pdb=" N SER G 108 " pdb=" CA SER G 108 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 9425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1471 0.043 - 0.085: 605 0.085 - 0.128: 274 0.128 - 0.171: 56 0.171 - 0.213: 12 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CB THR A 531 " pdb=" CA THR A 531 " pdb=" OG1 THR A 531 " pdb=" CG2 THR A 531 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB THR B 531 " pdb=" CA THR B 531 " pdb=" OG1 THR B 531 " pdb=" CG2 THR B 531 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE B 444 " pdb=" CA ILE B 444 " pdb=" CG1 ILE B 444 " pdb=" CG2 ILE B 444 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2415 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 351 " 0.026 2.00e-02 2.50e+03 2.19e-02 9.60e+00 pdb=" CG TYR B 351 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR B 351 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 351 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 351 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 351 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 351 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 351 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " -0.026 2.00e-02 2.50e+03 2.19e-02 9.60e+00 pdb=" CG TYR A 351 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU G 164 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO G 165 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 165 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 165 " -0.034 5.00e-02 4.00e+02 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3037 2.78 - 3.31: 13294 3.31 - 3.84: 26447 3.84 - 4.37: 30150 4.37 - 4.90: 53579 Nonbonded interactions: 126507 Sorted by model distance: nonbonded pdb=" OG SER A 298 " pdb=" O GLY A 301 " model vdw 2.248 2.440 nonbonded pdb=" OG SER B 298 " pdb=" O GLY B 301 " model vdw 2.248 2.440 nonbonded pdb=" OG1 THR B 135 " pdb=" OG SER D 134 " model vdw 2.258 2.440 nonbonded pdb=" O ALA A 223 " pdb=" OH TYR A 291 " model vdw 2.267 2.440 nonbonded pdb=" O ALA B 223 " pdb=" OH TYR B 291 " model vdw 2.267 2.440 ... (remaining 126502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 14.130 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 47.120 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.008 0.082 15620 Z= 0.544 Angle : 0.904 9.995 21270 Z= 0.488 Chirality : 0.056 0.213 2418 Planarity : 0.008 0.070 2724 Dihedral : 8.924 74.149 5670 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.17), residues: 1966 helix: -1.98 (0.26), residues: 232 sheet: -2.29 (0.18), residues: 686 loop : -2.30 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G 119 HIS 0.005 0.001 HIS B 281 PHE 0.024 0.004 PHE A 466 TYR 0.053 0.003 TYR B 351 ARG 0.008 0.001 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9123 (m-30) cc_final: 0.8298 (p0) REVERT: F 115 PHE cc_start: 0.5608 (m-80) cc_final: 0.5036 (m-80) REVERT: G 160 ASP cc_start: 0.9124 (m-30) cc_final: 0.8297 (p0) REVERT: H 115 PHE cc_start: 0.5606 (m-80) cc_final: 0.5033 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3190 time to fit residues: 129.7052 Evaluate side-chains 153 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN F 90 GLN F 123 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS A 358 GLN A 423 ASN C 141 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 GLN H 90 GLN H 123 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS B 358 GLN B 423 ASN D 141 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15620 Z= 0.220 Angle : 0.626 8.805 21270 Z= 0.329 Chirality : 0.046 0.181 2418 Planarity : 0.006 0.058 2724 Dihedral : 5.616 45.467 2124 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 1.43 % Allowed : 6.80 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.18), residues: 1966 helix: -0.26 (0.34), residues: 232 sheet: -1.88 (0.18), residues: 716 loop : -1.91 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 119 HIS 0.004 0.001 HIS B 281 PHE 0.017 0.002 PHE C 148 TYR 0.018 0.002 TYR A 351 ARG 0.006 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9045 (m-30) cc_final: 0.8402 (p0) REVERT: F 4 MET cc_start: 0.8627 (mmm) cc_final: 0.8403 (mmp) REVERT: F 92 TYR cc_start: 0.7718 (t80) cc_final: 0.7260 (t80) REVERT: C 113 ASP cc_start: 0.7219 (t0) cc_final: 0.7014 (t0) REVERT: G 160 ASP cc_start: 0.9048 (m-30) cc_final: 0.8403 (p0) REVERT: H 4 MET cc_start: 0.8623 (mmm) cc_final: 0.8400 (mmp) REVERT: H 92 TYR cc_start: 0.7729 (t80) cc_final: 0.7266 (t80) outliers start: 25 outliers final: 9 residues processed: 183 average time/residue: 0.2997 time to fit residues: 79.6277 Evaluate side-chains 142 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 0.4980 chunk 60 optimal weight: 0.0970 chunk 143 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15620 Z= 0.208 Angle : 0.579 11.763 21270 Z= 0.299 Chirality : 0.046 0.152 2418 Planarity : 0.005 0.055 2724 Dihedral : 5.215 43.335 2124 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.71 % Allowed : 7.31 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.18), residues: 1966 helix: 0.27 (0.35), residues: 232 sheet: -1.71 (0.18), residues: 724 loop : -1.69 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 119 HIS 0.008 0.001 HIS E 113 PHE 0.019 0.002 PHE A 148 TYR 0.024 0.002 TYR E 51 ARG 0.004 0.001 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9015 (m-30) cc_final: 0.8382 (p0) REVERT: F 92 TYR cc_start: 0.7624 (t80) cc_final: 0.7146 (t80) REVERT: A 462 THR cc_start: 0.8344 (p) cc_final: 0.8138 (p) REVERT: G 160 ASP cc_start: 0.9016 (m-30) cc_final: 0.8381 (p0) REVERT: H 92 TYR cc_start: 0.7633 (t80) cc_final: 0.7151 (t80) REVERT: B 462 THR cc_start: 0.8376 (p) cc_final: 0.8173 (p) outliers start: 30 outliers final: 16 residues processed: 165 average time/residue: 0.3022 time to fit residues: 72.7626 Evaluate side-chains 148 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15620 Z= 0.226 Angle : 0.566 9.196 21270 Z= 0.291 Chirality : 0.045 0.163 2418 Planarity : 0.004 0.052 2724 Dihedral : 4.990 41.326 2124 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 1.71 % Allowed : 8.51 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.18), residues: 1966 helix: 0.71 (0.35), residues: 232 sheet: -1.50 (0.18), residues: 718 loop : -1.40 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 119 HIS 0.006 0.001 HIS E 113 PHE 0.016 0.001 PHE A 148 TYR 0.033 0.001 TYR G 51 ARG 0.004 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9037 (m-30) cc_final: 0.8438 (p0) REVERT: F 92 TYR cc_start: 0.7593 (t80) cc_final: 0.7109 (t80) REVERT: A 455 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: G 160 ASP cc_start: 0.9039 (m-30) cc_final: 0.8436 (p0) REVERT: H 92 TYR cc_start: 0.7607 (t80) cc_final: 0.7115 (t80) REVERT: B 455 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7281 (tm-30) outliers start: 30 outliers final: 16 residues processed: 155 average time/residue: 0.3112 time to fit residues: 69.8616 Evaluate side-chains 127 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 0.3980 chunk 130 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 423 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15620 Z= 0.386 Angle : 0.621 6.928 21270 Z= 0.321 Chirality : 0.046 0.153 2418 Planarity : 0.005 0.052 2724 Dihedral : 5.070 42.922 2124 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.61 % Rotamer: Outliers : 2.17 % Allowed : 9.09 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1966 helix: 1.04 (0.35), residues: 222 sheet: -1.51 (0.18), residues: 738 loop : -1.16 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 119 HIS 0.007 0.001 HIS G 113 PHE 0.043 0.002 PHE A 148 TYR 0.038 0.002 TYR E 51 ARG 0.005 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9071 (m-30) cc_final: 0.8527 (p0) REVERT: F 168 LYS cc_start: 0.7223 (pttt) cc_final: 0.5801 (pttt) REVERT: F 194 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: A 318 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7257 (ttp-170) REVERT: A 455 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: G 160 ASP cc_start: 0.9071 (m-30) cc_final: 0.8527 (p0) REVERT: H 168 LYS cc_start: 0.7226 (pttt) cc_final: 0.5805 (pttt) REVERT: H 194 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7425 (pp20) REVERT: B 318 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7259 (ttp-170) REVERT: B 455 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7418 (tm-30) outliers start: 38 outliers final: 24 residues processed: 148 average time/residue: 0.2886 time to fit residues: 62.8532 Evaluate side-chains 140 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.1980 chunk 170 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 0.1980 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15620 Z= 0.184 Angle : 0.552 7.444 21270 Z= 0.284 Chirality : 0.045 0.153 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.829 40.164 2124 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.71 % Allowed : 9.83 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 1966 helix: 1.33 (0.36), residues: 222 sheet: -1.33 (0.18), residues: 746 loop : -1.03 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 48 HIS 0.004 0.001 HIS B 333 PHE 0.017 0.001 PHE A 148 TYR 0.026 0.001 TYR E 51 ARG 0.004 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9037 (m-30) cc_final: 0.8502 (p0) REVERT: F 168 LYS cc_start: 0.7113 (pttt) cc_final: 0.5652 (pttt) REVERT: F 194 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: A 455 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: G 160 ASP cc_start: 0.9038 (m-30) cc_final: 0.8500 (p0) REVERT: H 168 LYS cc_start: 0.7120 (pttt) cc_final: 0.5657 (pttt) REVERT: H 194 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7464 (pp20) REVERT: B 455 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7220 (tm-30) outliers start: 30 outliers final: 18 residues processed: 145 average time/residue: 0.2730 time to fit residues: 59.5152 Evaluate side-chains 131 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 118 optimal weight: 0.0270 chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15620 Z= 0.331 Angle : 0.601 8.579 21270 Z= 0.308 Chirality : 0.045 0.148 2418 Planarity : 0.004 0.051 2724 Dihedral : 4.865 40.454 2124 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 1.83 % Allowed : 10.00 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1966 helix: 1.42 (0.36), residues: 222 sheet: -1.31 (0.19), residues: 738 loop : -0.97 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 48 HIS 0.003 0.001 HIS H 188 PHE 0.015 0.002 PHE B 290 TYR 0.049 0.002 TYR E 51 ARG 0.005 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9044 (m-30) cc_final: 0.8529 (p0) REVERT: F 168 LYS cc_start: 0.7130 (pttt) cc_final: 0.5717 (pttt) REVERT: F 194 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: A 455 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: G 160 ASP cc_start: 0.9046 (m-30) cc_final: 0.8528 (p0) REVERT: H 168 LYS cc_start: 0.7138 (pttt) cc_final: 0.5727 (pttt) REVERT: H 194 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: B 455 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7329 (tm-30) outliers start: 32 outliers final: 28 residues processed: 135 average time/residue: 0.2808 time to fit residues: 57.9514 Evaluate side-chains 138 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 15620 Z= 0.497 Angle : 0.684 7.583 21270 Z= 0.352 Chirality : 0.047 0.159 2418 Planarity : 0.005 0.051 2724 Dihedral : 5.240 45.722 2124 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.97 % Favored : 92.93 % Rotamer: Outliers : 2.40 % Allowed : 9.71 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1966 helix: 1.35 (0.35), residues: 218 sheet: -1.32 (0.19), residues: 734 loop : -1.08 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 37 HIS 0.005 0.001 HIS G 113 PHE 0.016 0.002 PHE B 290 TYR 0.047 0.002 TYR E 51 ARG 0.005 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9033 (m-30) cc_final: 0.8605 (p0) REVERT: F 168 LYS cc_start: 0.7337 (pttt) cc_final: 0.5912 (pttt) REVERT: F 194 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: A 455 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: C 139 ASN cc_start: 0.8005 (m-40) cc_final: 0.7687 (t0) REVERT: G 160 ASP cc_start: 0.9034 (m-30) cc_final: 0.8608 (p0) REVERT: H 168 LYS cc_start: 0.7345 (pttt) cc_final: 0.5918 (pttt) REVERT: H 194 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: B 455 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7458 (tm-30) outliers start: 42 outliers final: 36 residues processed: 144 average time/residue: 0.2709 time to fit residues: 61.4093 Evaluate side-chains 139 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 99 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 585 ASP Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.8980 chunk 180 optimal weight: 0.0370 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 159 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15620 Z= 0.181 Angle : 0.581 11.803 21270 Z= 0.293 Chirality : 0.045 0.138 2418 Planarity : 0.004 0.046 2724 Dihedral : 4.888 42.656 2124 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.49 % Allowed : 10.63 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1966 helix: 1.69 (0.36), residues: 222 sheet: -1.21 (0.19), residues: 734 loop : -0.82 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 119 HIS 0.003 0.001 HIS G 113 PHE 0.011 0.001 PHE H 138 TYR 0.034 0.001 TYR E 51 ARG 0.004 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9012 (m-30) cc_final: 0.8497 (p0) REVERT: F 168 LYS cc_start: 0.7195 (pttt) cc_final: 0.5770 (pttt) REVERT: F 194 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: A 399 MET cc_start: 0.8708 (mmt) cc_final: 0.8492 (mmt) REVERT: A 455 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: G 160 ASP cc_start: 0.9016 (m-30) cc_final: 0.8498 (p0) REVERT: H 168 LYS cc_start: 0.7198 (pttt) cc_final: 0.5774 (pttt) REVERT: H 194 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: B 399 MET cc_start: 0.8694 (mmt) cc_final: 0.8420 (mmt) REVERT: B 455 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7176 (tm-30) outliers start: 26 outliers final: 20 residues processed: 134 average time/residue: 0.2540 time to fit residues: 52.6622 Evaluate side-chains 123 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 30.0000 chunk 186 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15620 Z= 0.234 Angle : 0.582 8.313 21270 Z= 0.294 Chirality : 0.045 0.186 2418 Planarity : 0.004 0.048 2724 Dihedral : 4.863 40.682 2124 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 1.31 % Allowed : 11.20 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1966 helix: 1.72 (0.36), residues: 224 sheet: -1.10 (0.19), residues: 730 loop : -0.77 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 48 HIS 0.005 0.001 HIS G 113 PHE 0.009 0.001 PHE E 80 TYR 0.047 0.002 TYR G 51 ARG 0.005 0.001 ARG H 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9029 (m-30) cc_final: 0.8508 (p0) REVERT: F 168 LYS cc_start: 0.7205 (pttt) cc_final: 0.5771 (pttt) REVERT: F 194 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: A 455 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: G 160 ASP cc_start: 0.9033 (m-30) cc_final: 0.8510 (p0) REVERT: H 168 LYS cc_start: 0.7209 (pttt) cc_final: 0.5777 (pttt) REVERT: H 194 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: B 399 MET cc_start: 0.8735 (mmt) cc_final: 0.8447 (mmt) REVERT: B 455 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7182 (tm-30) outliers start: 23 outliers final: 19 residues processed: 121 average time/residue: 0.2437 time to fit residues: 47.0453 Evaluate side-chains 125 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 155 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.090716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.060120 restraints weight = 48808.746| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.98 r_work: 0.3084 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15620 Z= 0.203 Angle : 0.566 8.359 21270 Z= 0.286 Chirality : 0.045 0.162 2418 Planarity : 0.004 0.047 2724 Dihedral : 4.737 37.537 2124 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.26 % Allowed : 11.26 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1966 helix: 1.83 (0.36), residues: 224 sheet: -1.00 (0.19), residues: 732 loop : -0.71 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 48 HIS 0.004 0.001 HIS G 113 PHE 0.019 0.002 PHE H 115 TYR 0.040 0.001 TYR G 51 ARG 0.005 0.001 ARG F 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3516.38 seconds wall clock time: 64 minutes 40.22 seconds (3880.22 seconds total)